I was thinking the same thing when it comes to wiring up my ES-1 kit.[mini Bournes that is ]

I'm guessing you use the plastic tubing method for pulling the pots into the mounting holes ? It seems the least troublesome way to go about it.
Is there a specific 'Best Practice' for installing the wiring through the F hole that you could recommend?, like a particular order, say Jack plug, then Tone/Tone/Volume/Volume ?

I briefly had a half hearted look at cutting a hole in the bridge pickup hole area, for possible mounting the pots that way, but I saw how close the holes are for the bridge mounting bushings, and thought if I did try it, I might undermine the strength of that area, so have decided against it

Come the big wiring up day, I'll have a swear jar, punching bag, and if worse comes to worse, some Valium handy