Yes, it is back under the knife! I filled the post holes today with Titebond 2 and maple dowels.It's a matter of "how much." If the intonation is so off that saddle travel is maxed, then small tweaks will not do it, and you will have no room for future adjustments anyway. If you mis-located the unit, as it seems you did, then filling it in and recutting is what should be done. You should now be able to calculate closely how far you need to move the unit to get the saddles positioned more towards the middle of the travel area. As for intonation work at the nut, I've done it with excellent results, but this is far too much a fine-tuning process ("polish") than is needed to cure your basic difficulty, which appears to be a macro mis-positioning of a whole unit. I'm sorry it happened, but I would do the full remedy.
And it certainly will be easier to find the sweet spot for the bridge this time around. Only minor issue is the front edge of the bridge will encroach on the pickguard.
I hate cutting those things. I have messed up so many from burning with dremel tools or funky looking cuts