There's more going on here than you think.
In the bad old days, all we had was the plain old thermal-magnetic circuit breaker (or worse yet, thermal-only fuses for folks with old stuff). Folks got zapped by hairdryers dropped into bathtubs and watched as poor connections and damaged cords turned their house into a bonfire for the local FD.
In the 70s, as microcircuit technology developed, the Ground Fault Circuit Interrupter was introduced. These devices use electronics along with a current transformer to measure the difference between hot and neutral, and open the circuit if it is excessive -- in the power distribution world, the equivalent function is called a "differential trip". UL set two trip thresholds for these devices -- 6mA for protection of personnel (the GFCI we find in our bathrooms), and 30 or 100mA for protection of equipment (a so-called Ground Fault Protector for Equipment, or GFPE, device). The GFCI was made available in both a receptacle form factor, originally intended for "quick fix" retrofits, and a circuit breaker form factor, originally intended for new construction or GFCI applications outside the scope of 15 and 20A receptacles. GFPEs, however, were only made available in breaker form as they are used in a limited set of applications, mainly to protect long heating cable/tape runs or high-powered feeders where ground faults can cause serious fires.
Fast-forward 20-odd years now, into the late 90s. Microcircuit and microcomputer technology has advanced significantly, and GFCIs have become a well-known part of house wiring, deployed in a variety of wet and damp location applications. Dropping a toaster into the bathtub becomes futile as an assassination method. However, houses are still burning down from electrical faults, aggravated by postwar copper shortages causing AA-1000 wiring and steel screws to be pressed into dwelling unit service for a time in the 60s (aka the aluminum wiring debacle). However, the use of GFPEs on high powered feeders has proven to be a successful fire protection measure in that arena, and some testing performed by CPSC and UL revealed that damaged cords and wires were a major problem for house fires.
Enter the first generation Arc Fault Circuit Interrupter (AFCI). These devices were based on a mixture of analog and digital technologies, and proved highly effective at detecting house-burning parallel arcs, but in order to detect other fire-starting conditions, such as glowing connections, they also had to add the equivalent of GFPE protection into the device. While not enshrined in the UL standards for AFCIs (a rather...debatable requirement for "series arc detection" was substituted for it, at least for the combination type AFCIs commonly deployed), most AFCI makers incorporated this functionality into their devices. (Branch/feeder AFCIs lack series arc functions, relying solely on the GFPE trip to provide protection against glowing connections and other leakage inducing faults.)
However, the AFCI/GFPE combination had a drawback -- people were expecting it to behave like a regular single pole breaker, not a GFPE, and were perplexed by mystery trips when they started installing it. While some of these mystery trips were due to arc-generating devices not being distinguished from real arcs, or EMI, some of them were a function of shared and looped neutrals in house wiring as a result of wiring errors. This, of course, was all blamed on the AFCIs, rightly or wrongly, and also led to GE eventually redesigning their AFCI products to remove the GFPE functionality, replacing it entirely with microcomputer-based series arc detection.
Fast forward another 10 years. The AFCI requirement, while still debated at the local level, has become permanently enshrined in the NEC, and is being expanded much like the GFCI requirement was back in the 80s. One spot AFCI protection was expanded to during this was the kitchen -- with high power appliances, extensive usage, and all sorts of cord damage possibilities, the possibilities for electrical fires abounded here. This, however, collided with the existing requirement for GFCI protection -- you either had to put one of the protection devices in a receptacle form factor (usually the GFCI), or use a subpanel to house a second, series-connected breaker with its attendant hassles. Hence, in the early 2010's, manufacturers started to introduce Dual Function Circuit Interrupter (DFCI) devices that combined combination-type AFCI protection with GFCI protection for personnel. While only available for single phase, 15 and 20A branch circuits at this time, they represent the ultimate in protection.
Furthermore, receptacle (called "outlet branch circuit") AFCIs were developed for retrofit and other limited (such as part of what is called a "system combination AFCI" using a specially listed circuit breaker, supplemental arc fault circuit breaker, or branch/feeder AFCI) applications. There is even a receptacle DFCI on the market, but its application scope is unclear.
Can you have more protection than the bare minimum?
The answer to this question is almost a resounding yes. The main caveats with installing AF/personnel GF protection throughout a building are leakage currents, EMI, and shared neutrals/MWBCs. Once these are licked, then full ground and arc fault + overcurrent and short circuit protection throughout a building can be a reality.
First, some appliances have poor AF/GF compatibility. They generate arcs internally that are mistaken for arc faults, spit EMI onto the power line that confuses sophisticated trip sensors, or simply leak too much current to ground. Once again, though, instead of taking, say, the vacuum back because it's tripping the arc fault breaker for their bedroom, people blame the breaker for the problem -- this has been a cause of serious pushback against AFCI mandates, and is even a problem with plain GFCIs in corner cases.
The other problem is shared neutrals and MWBCs. Shared or looped neutrals are the result of common wiring errors, usually "nut all the whites together" in boxes which are fed by more than one circuit. A simple solution is to keep separate circuits completely separate, but this isn't always practical (say for kitchen small appliance branch circuits). Fortunately, another option is available -- nowadays, you can buy two circuit (/2/2) NM cable that has two distinctly identified neutral wires in it, which can help with this, and also provides a suitable substitute for the use of MWBCs, as two-pole DFCIs are not available despite two-pole AFCIs and GFCIs being stock items.
AFCIs are also a bit like GFCIs in that they care a lot about crossed neutrals. A LOT. You will never get any AFCI to hold while a crossed neutral persists, nor should you! Remember, neutrals do not have breakers, the only thing that keeps them from overloading is the fact that they are fed from only one hot. If they are fed by 3 hots, one could return 45A and of course start a fire in the walls.
You will have to identify every outlet (including hardwired ones) on each circuit. Pull the covers off and the devices out. Document how they are wired. It is likely you will uncover the problem at that point.
If not, disconnect them all and light up each circuit, one at a time, to determine which is the "first" outlet. Hook up that outlet correctly (as opposed to how it is now) and test. Continue one at a time, thoroughly testing each time.
When you run out of things to hook up, and you still don't have problems, then you have licked it. Otherwise, the problem will return at a particular step. That is your problem area.
You seem sanguine about some crossed circuits in a 3-way light circuit. That may be one of your problems, and there may not be a legit way to regain original functionality without going to smart switches.
Best Answer
I think this is an over generalized thought. Since you mentioned 480, many industrial equipment sets using variable frequency drives require class j fuses for protection, their are still some AC units that state max fuse size (most have changed to max fuse or hvacr breaker in the last few years) in these cases it would violate the listing to use a breaker. I have updated quite a few homes in my area from fused to breakers because of insurance requirements but there are still companies that will insure homes with fuses or even FPE stablock panels, where fuses would be safer if properly sized in my opinion. I think the bigger problem is on fused system k&t or cloth wrapped wire was used and some of that insulation is failing being the root cause of the problem.