Spaces vs Circuits
First let's explain the 8/16 thing, or "8 spaces but 16 circuits". At some point, panel manufacturers developed what I (alone) call a "double-stuff" breaker, which crams 2 breakers into a single space. This is intended to solve crowding problems in too-small panels.
photo source: Home Depot
Relying on these, marketing called their boxes 2X-circuit (X-space). Around 2014 they mysteriously stopped doing that. Recent NEC changes required AFCI or GFCI breakers on damn near every circuit... AFCI and GFCI are not made in double-stuff breakers.
Your 16/8 service panel is a legacy of that bad labeling. You have an 8-space panel, intended to replace an 8-space fuse box.
Panel space is dirt cheap. Go nuts.
You are dreaming of a 16-space panel. And even that is dreadfully small and you will find it rather limiting even with 100A service.
The practice of many electricians is to give you the smallest panel possible. That's first, to force you into more subpanel work if you expand further (more money for them) and second to save themselves $20 in part cost.
The cost of a larger panel is trivial tiny compared to total project cost. It is very correct to be extreme. Please spend an extra $100 for a 42-space panel, unless you just can't make it fit. Honestly I'd go 60-space. Not least, those larger panels are 225A-ready.
You never know. You might do a kitchen remodel and go hey, I'd like a separate circuit for refrigerator done microwave done dishwasher done disposal done 3 outlet circuits done. You have the space.
When you buy a PC, do you really calculate your needed hard drive space and buy just what you need... Or do you just buy the big 3TB drive? Of course you do. Same thing here.
More work to do at the meter
OK so the power company says their side of the cable is 320A. If they say so.
They say their meter is 320A. If they say so.
But your meter housing is not 320A.
To support more than the listed 125A, you will need to upgrade your meter housing. There's no question of that. That's your equipment and you have to pay for it, probably, unless your power company does something different with cost sharing.
You won't be able to replace parts of it, you will probably even have to replace both sides of it as a single unit. However it is very nice to have your main breaker in the meter. It means you can fully de-energize your main panel, which makes it safer for you to do yourself.
The 320A may be shared
Since it's multi-unit, the power company provisioning 320A makes more sense. Trouble is, this 320A service is probably shared between both units. So it's not as much as you think.
You really need to talk to your power company about what they consider this "320A" to be. It may be a relabeling of what other power companies call 400A service. So they may be willing to feed two 200A panels, or 100/100/200. This is a conversation you can have only with them.
More food for thought is sub-metering units, and separately metering common spaces. The new thing in rental properties is to have one main meter and the landlord has sub-meters per tenant. Many landlords prefer (and some law requires) commons space usage to be on a separate (sub) meter, i.e. heating, yard and commons lighting, anti-freeze pipe wrap or roof/gutter heat, coin laundry, Christmas decorations etc.
First things first -- commingling service and non-service conductors in an auxiliary gutter is unwise, despite being Code-legal, so you were right to correct that situation.
Second, the grounding electrode conductor (and water system bonding termination) connecting into the meter pan grounding busbar is almost OK even though no separate EGC is routed from the meter pan to the service disconnects, as it falls under 250.64(D)(3):
(3) Common Location. A grounding electrode conductor
shall be connected in a wireway or other accessible enclosure on the supply side of the disconnecting means to·one
or more of the following, as applicable:
(1) Grounded service conductor(s)
(2) Equipment grounding conductor installed with the
feeder
(3) Supply-side bonding jumper
The connection shall be made with exothermic welding or
a connector listed as grounding and bonding equipment. The
grounding electrode conductor shall be sized in accordance
with 250.66 based on the service-entrance or feeder conductor(s) at the common location where the connection is made.
My prime concern here would be that that ground busbar may not be accessible due to the utility seals on the meter pan -- if that part of the meter pan is customer accessible though, then that's not an issue.
Third, the gutter bonding arrangement follows 250.80 and 250.92, so that's hunky-dory, except for the fact that the 6AWG copper wire used is one size too small -- 4AWG is the correct size system bonding jumper as per table 250.102(C)(1).
Finally, the bond conductor between the gutter bonding point and the service disconnecting means is...redundant. 250.92(B)(1) calls for service equipment enclosures to be bonded to the grounded conductor using a Code-compliant means, and the green screw in your service disconnect enclosure's neutral bar certainly qualifies!
So, you can remove the redundant (and undersized) bonding jumpers in the auxiliary gutter, as well as the existing gutter bonding jumper, and use a length of 4AWG bare copper to bond the gutter to an accessible point on the grounded conductor (such as the existing meter pan grounding busbar) as per option 1 in your drawings. If the existing meter pan grounding busbar is indeed inaccessible, then the grounding electrode (GEC) and water system bonding conductors will need to be replaced with longer ones that can be run into the auxiliary gutter, as that's where a grounding tap for this stuff will need to be installed, connecting the service neutral to the GEC, water system bond, and gutter.
Your Option 2, however, probably won't fly -- the use of a separate bonding conductor alongside the service conductors might get dinged by the AHJ as a 250.92(B) violation, and is a waste of copper anyhow! (In fact, a cleaner solution than Option 2 would be to remove the dang PVC nipples and replace them with rigid metallic ones fitted using listed bonding-type locknuts.)
As to your updated plan, that appears mostly correct -- 4AWG is big enough for the job as per table 250.66, while the bond of the grounded neutral conductor to the meter pan is in accordance with 250.80 and 250.92. However, I would route the grounding wires for the CATV and telephone systems directly to the gutter grounding and bonding busbar, using it as your intersystem bonding termination as well. This treats the auxiliary gutter as "an enclosure for service equipment" for the sake of 250.94 and eliminates the need to make irreversible compression-type or exothermically welded taps on the new grounding electrode conductor. Finally, I would remove the existing grounding electrode conductor and water system bonding conductor to avoid inadvertently paralleling the neutral and possibly causing stray currents in the water piping or grounding electrode systems.
Best Answer
You can cut a hole through the back, with a nipple less than 24" long you can fill it to 60%, it's hard to tell from the photo what the fill is, in the past with exterior boxes I have punched 2-3 holes installed bushings and run my wiring from a gutter where I spliced it to some thhn/ thwn and ran that outside. In my last county the inspector felt it was safer not to splice in the gutter and to run the romex into the outside service panel, I would check with your local inspector as they may allow the romex into the service panel (2 out of 3 counties allow this to a nema 3R service panel in my area). The panel must be mounted on the dwelling so the wires directly enter the home.