Once the transom is supporting the aft end and the bottom panels are screwed/glued to the stringers, you'll want to take a look at things then. I expect some variation to occur, but this is OK. Trust your eyes. You want fair curves where curves exist and straight runs aft. If you're careful to guarantee straight runs on the chine flats before you lock them in by installing the side panels, then you're good. If after building the exterior hull seams and you're getting ready to add the sheathing (glass cloth) over the whole outside of the boat, then that's when you want to give it all a careful analysis and fix any hollows and fair-in any minor humps. It's not unusual to need to fill and fair - it's a big boat, unlikely to be naturally flat everywhere you look. Once the hull has been faired the first time, and you've glassed the whole thing, you'll again look at it all carefully, sighting the long way (fore to aft and vice versa) to look at the bottom etc before putting final epoxy coats on. You want 2 coats on top of any fairing compound or mix that you apply.
Can you take some longer perspective pictures of your boat? It's hard to tell for sure what you're pointing out. As far as I know, nobody's tried fitting bottom panels onto the assembly after putting it on the stringers. I care mostly that all curves are fair rather than how precisely the bottom fits the molds now that it's not supported in the same way.
Brian