I thought the ballistic advantage of BT bullets at longer range cf. shorter range was because was because of the improved BC resulting from the BT shape, rather than any disadvantage from the BT shape at shorter range - though srvet's point about the bullet 'going to sleep' quicker with a flat base is interesting.
The evenness of the gases passing the bullet after it leaves the muzzle is AFAIK a property of the crown. The bullet's base which the gases are passing will be revolving at 180,000rpm - so minor unevenness there will be averaged out fairly well, I'd imagine.
Although spinning very fast, the bullet is only making one turn in the length of your rifle's twist. E.g it will have to have travelled 12", 10", 8" or whatever, from the muzzle, to have made just one rotation. So no, I don't think that it averages out.
The muzzle blast does overtake the bullet initially, but it's soon left behind.
If you use a moderator or muzzle brake, that could also greatly affect what happens in those first few inches from the muzzle. What gas flow goes on inside a moderator, whether that might buffet the bullet, I can only speculate.
The crown is all-important. The perfection of the bullet base too, equally so I'd guess, flat bases are supposed to be less difficult to make consistent than boat tails, but I suspect that the differences with good bullets aren't huge. And it could rather depend on the gas pressure behind it just as the bullet leaves the muzzle, which is largely a function of powder choice, loading, and burn characteristics.
The good news is that whilst all bullets leave the muzzle slightly cock-eyed, even from supposedly perfect match barrels with match chambers, 11 degree target crowns, and trued straight actions, they do stabilise ("go to sleep"), assuming that they are well made and suited to the velocity and twist. That may take some distance though.
My limited experience with .223 was that flat bases were the most accurate to say 300 yards, beyond that the boat tail designs started to show their advantages.
Once they are in the air, the perfection of the pointed end is all-important. . This is where the shock wave starts, any imperfection here has the potential to send them off-course. The shock wave moves back down the bullet onto the ogive as it slows, even towards the tail, but whilst it remains highly supersonic the effect at the tail is I suspect less of a factor, though still important. It's the overall shape that matters, boat tails do help here, the better ones are shaped to minimise "drag", i.e. the energy dissipated in creating the shock wave. Subsonic or trans-sonic designs, well that's a different subject.
Here's some Schlieren photography demonstrating this:
Flat bases generally carry their mass to the rear, boat tails can help distribute it further forwards, which is supposed to be better at longer range. You can also over-stabilise a bullet if you spin it faster than necessary, then it won't stay in line with it's trajectory, becoming increasingly angled up as range increases, with increasing drag and other bad effects.
Hornady make quite some claims for their ELD-X bullets, take a look at
Heat Shield® Technology - Hornady Manufacturing, Inc for example.