That's a good reason to leave the rifling in place all the way to the bottom. And, a good reason to get your vent liner as close to the breech as possible. If you use a 1/4" vent liner, the hole will be 1/8" forward of the back of it.
In larger calibers, like a 50 cal, that means it's 1/4" from the bottom of the ball to the ogive. If you get your vent liner tight to the breech plug, you should have some space to fish some powder in that little nook when you dry ball.
Obviously, the further you put the liner from the plug the less room you will have. In larger calibers you have more margin for error than the smaller ones, like a 32. There is just no way you could ever get the liner tight enough that you could engineer in a space below the ball ogive in that case. I shoot a 38 mostly (and am yet to dry ball it) but think it unlikely I'll have an alternative to pulling the ball once I finally DO dry ball it.
If you grind out the rifling down there, with that small amount of powder you fish in through the vent, the burning gas may escape through the patch or around the ball (as well as through the vent) and not expel it.
Honestly, I can't see many benefits to reaming out the rifling in the first place. It will be harder to keep it all clean at the end of a shooting session, and the amount of reaming wouldn't be enough to gain you the efficiency in combustion that a bottle necked cartridge has.
One other way to increase it though would be to dish out your breech plug to direct the pressure forward, like a shaped charge works. You'll get higher velocities with the same powder charge that way. The down side is that cleaning the plug face will be just that much trickier. I don't think the trade-off is worth the effort personally, but to each their own.