A cap per tone pot doesn't really matter - you get this arrangement in many other guitars, especially Gibsons. Leo Fender was a real penny-pincher and used the least number of components he thought he could get away with (e.g. Telecasters moved from 5 to 8 screw pickguards after a few years because the original 5 wasn't enough to stop the guards warping over time), so used a circuit that shared the capacitor between tone pots. No idea why the PBG kits do it differently but the result is basically the same. If I was upgrading pots and caps I'd re-wire it to the Fender standard method, but otherwise I'd leave it as it is.
Audio vs linear tone pots? All depends if you actually use the pots or not. If you always have them set on 10, it makes no difference whatsoever. But if you do play with the tone knobs, then linear pots (the generally selected pot type for tone use) will give you a noticeably darker tone for a small initial movement e.g. from 10 to 8, compared to an audio taper which might take turning from 10 to 4 to get the same darkening of tone. When set to 0, both pots give the same level of maximum dullness.
You can obviously get the same level of darkness in the tone using either style pot, it's just a matter of by how much you have to turn the knob to achieve it.
So if you occasionally like to just knock the edge off the brightness, then an audio taper would probably be the best choice, but if you are a regular tone pot adjuster and like to hear a difference quickly, then linear is probably the better choice.