Limitations of CNC machining leave some aspects of fitting parts up to the builders, just as if they were getting parts out from plans. I had same challenge fitting drive trunk cover when assembling my Waterlust; it's expected that some material is to be removed where fillets create interference with what comes next.

If sanding'll do it, by all means proceed! In my case I chose my Shinto rasp, then sandpaper once I was closer. Even if you go a bit too far the thickened epoxy you'll use to bond doublers in place will fill any gaps nicely. No worries in that regard!

   Yeah, right, thank you. I said it feels silly because if I realized that in advance, I would've just skipped the parts of my fillets overlaping with the transom doublers... and now, instead, I have a separate project on my hands. Oh well.

Yes, I had the same issue when building my EP.  Just shape the doublers so they fit, then epoxy in place.