If you're sidestepping the clutch, that's bad, hard on everything from the clutch center to the differential, but unlikely to be catastrophic. If you're just talking about a little bit of unsettling, then that for all practical purposes that's nothing to worry about. A good upshift will always be a little firm. Downshifts you want to modulate a little more, especially if it's mid-corner, but I doubt you're pushing it hard enough to worry about that.
As far as over/under, I don't see a reason why it would make much difference overall. If you're still applying power and it's over, I can see that wearing the clutch slightly more (since the engine is giving even more than usual resistance to changing RPM due to the extra throttle you're applying), but I doubt that's the case.
Honestly, you're probably over-thinking it. I always shift best if I'm just not giving it conscious thought.
ZV