I've used basswood to plug up the ends of a pickup rout in a JB kit as the pickups I'm using are shorter but wider than the standard JB pickups. I used Titebond to glue it in place, then filled the gaps with an UV-curing resin. Then sanded the top flat and routed out to the right size. With primer and paint on top, you'd never know.

Wood doesn't breathe, but it can dry out or absorb moisture, which is one good reason for putting a finish on the guitar, to prevent this happening as much as possible and stop it shrinking or expanding slightly with changes in climate conditions.

I've never used Bondo itself, but I've used similar products for filling and you should be fine with it.