Differences in apparent accuracy at 100 yards may not show up wrt type of bullet, whereas at long range, they will, a lot more clearly (effects of drag and stability over time on the bullet) and in terms of rifling design, I've yet to be convinced that new designs of rifling are any better than traditional rifling. Many BR records and high competition scores have been set which were shot on traditional cut, button or hammer forged rifling.
There are some new kids on the block in terms of rifling design (but even then, I think they're taking some older established rifling principles and simply applying them to mass manufacture for the first time). Sabati is one example, (with MRR already having been mentioned in the post above) having dispensed with traditional sharp edged rifling, and now using what they call Multi-Radial rifling which follows principles first proposed by Whitworth's polygonal rifling principle, but using hammer forged rounded profile for the lands. They are meant to be accurate and so-say tighten up groups but I have yet to see any comparative evidence of this against a more traditional rifled barrel, so the jury may be out on this. It's a tough market and marketing may play a part of grabbing a slice of the pie, or there may be merit in the design. Only some scientific rigour applied to comparative tests using the same bullets would convince me.
Any bullet shot from a "bad" rifle mightn't shoot for toffee, so just saying "it's not the bullet, it's the rifle" doesn't really address the question. There's a reason that top competition shots all either use hand made custom bullets or top Berger bullet types. Design, manufacturing tolerance and consistency. A bullet should ideally not deform in flight nor the jacket be so thin as to break up or be badly damaged by swaging. The argument for flat base against boat tail has more to do with long range advantages in lowering drag and maintaining stability. Flat base can be equally as accurate at closer ranges albeit will exhibit lower BC for any given length of bullet, so may be more affected by wind etc. Not a straight forward answer once the variables are considered!
Worth keeping an eye out though to see of MRR rifling becomes the norm.