Electrical – Is this an acceptable way to route wires around trusses

You're describing a shared neutral, and some local codes allow it, some don't. However, it's usually described with closely related circuits, like a single 12/3 wire feeding alternate receptacles in a kitchen's two 20A circuits.

In general, I think they're a bad idea because if circuits A and B share a neutral, you could potentially still have current in A's neutral with A turned off at the service panel. In addition, if A and B are on different phases and there's a problem with the neutral, you could have 240V across all your devices. Using a ganged breaker mitigates those risks somewhat.

How difficult would it be to replace the 14/3 between the switches with two 14/2 wires? That would get neutral to the downstairs switch and wouldn't raise any eyebrows come inspection time. If that would also be difficult, next step is to talk to an electrician that knows what's allowed in your area.

Of all the homes I help oversee the construction of, the main thing that was followed when it comes to lightning protection is no sharp bends in the cable, or uphill runs. Always going down to ground. It can be run through walls, by means of drilled holes through the plates, so a close proximity of a non conductive PVC will be no problem. If you want to be safe, get a small gap between the conduit and the cable, though I think it does not need to be much say 1/2"to an 1". Since static electricity carries over the surface of the wire and not through the wire, which is the reason the cable is loosely braided, a little space between the two should suffice, just to be sure.