Does the tail shape of the bullet matter that much while the bullet remains supersonic?  It seems like everything behind the forward ogive is going to be behind the bow wave anyway, while the bullet remains solidly supersonic.  I get the need for boattails when you hit the transonic range. 

Yes, the shape of the boattail is critical in supersonic flight. I have found substantial drag reductions (or increases) in Flow Sim are possible by adjusting the boattail angle, length, shape, and base. The boattail does not account for the majority of drag, but the notion that it's irrelevant to supersonic flight is erroneous. Particularly as velocities approach transonic (decreasing in speed, as a bullet does) the configuration of the boattail gets more and more important. I've been able to reduce drag by more than 15% in my latest ultra low drag projectiles, and much of that was via optimizing the boattail.

Boattail is also important at muzzle exit (uncork); supersonic propellant gases accelerate, diverge, and flow past the projectile (reverse flow) for a dozen calibers or more at launch. Square butt is more susceptible to slight upsetting forces resulting from surface imperfections and muzzle-crown irregularities. Spin-stabilized projectiles seem as susceptible as fin-stabilized. Usually a minor effect, but statistically notable. 

Well I know some match rifle bullets are flat base specifically because you can get a better gas seal and more consistent launch; they let less gas slip by.  I totally believe the base shape can have some drag effect even in supersonic flight, but I am just trying to wrap my head around how much.  I've dug around a lot looking for real chrono data and come up dry. 

Followup question: Say you had a 6mm fmj bullet, same nose shape, same overall length, same velocity; one was a 90 grain boattail, the other a 100 grain flat base.  Which would retain energy better during supersonic flight? 

In other words, to what extent would the added sectional density of the bullet counteract the increase in drag of the flat base?

I got to this question by just doing a though experiment re how much you could stretch the performance of the 6x45mm wildcat cartridge, where OAL is the real limitation if you want it to work in an AR platform.  Flat base bullets are shorter for the same weight, and most load data I could find is with boattail bullets, hence the question. 

JesseH1234 said:

Followup question: Say you had a 6mm fmj bullet, same nose shape, same overall length, same velocity; one was a 90 grain boattail, the other a 100 grain flat base.  Which would retain energy better during supersonic flight? 

Depends on the exact shape. The 90gr bullet would need a 10% better i7 than the 100gr bullet to equal it. That is possible, as I mentioned, optimizing boattail shape has earned me the bulk of a 15% improvement in drag, and that was just by optimizing boattail shape, not against flat based projectiles.