Please don't confuse me with the experts available here, but it's late and I'm up...(and I never crossed my bbl with a level)
Sounds completely irrelevant to me. The flats are not the bore-and the contours are just that. They are shapes added after the barrel was bored and rifled and maybe even on different machinery.
The alternative might be to drawfile it plumb-as best you can because you are committed to the side flats and would then have to transition corrections into them via the next higher flats without making a mess of parallelism. Of course you'll hereinafter be more cognizant of this possibility and like work on it during your draw-filing process for the desired result.
So, i'd sight it, drill it, mount it, and shoot it. Then pitch a hissie if it wouldn't group with a well-developed load.
I seriously expect it to shoot and your dilemma to be purely "cosmetic"-That is, only if others tend to notice. If they don't then it's
nothing