I don't have a lot to report from my own experience, but I pursued a similar line of inquiry to yours, and found two directions: 1) glue a chunk of wood into what you want to fill, or 2) fill it with Bondo, so some other mold-able/drill-able filler substance.
In the end, I decided that it was too much an affront to the original intentions of the designer, and it was better to just run with the the instrument's zeitgeist. Depends on the body. If it's a decent design unto itself, it seems right to me to preserve the original intent - making subtle hardware upgrades here and there, but nothing radical like filling gaps. But if it's a beater/test tube piece of machinery, why not do what you will with it?
Incidentally, I'll probably end up selling that guitar, because "what it is" is too out of line with what I like (and the neck is really nice, and the heel super comfy)...but I'll use it to test wiring/electronics on (it's a rear-route, so the soft white underbelly is vulnerable to multiple soldering iron attacks) for another year or so. The only thing saving it for trade-in now is sentimental value....