Broadly speaking opening a valve further reduces flow resistance, at least up to point but more travel means greater acceleration and thus greater forces on parts, which is magnified as RPM increases.
Indeed with mechanical valves you get to a point where the return springs can't act fast enough and you starts to get harmonic effects where the valves themselves are no longer directly coupled to the cams ie 'valve float' which can be pretty serious.
Equally it is entirely possible in high compression engines that the valves and piston occupy the same space so if timing isn't right they can collide. In mechanically driven systems this should only happen if something breaks or the design rpm is exceeded (see valve float above) although even then many pistons have small crescent shaped cutouts to allow valve clearance.
So the short answer is that the most important tolerance that the valves and pistons absolutely can't occupy the same space at the same time, everything else im more or less negotiable.
F1 engines have for a while now have used pneumatic valves as camshafts and springs just can't respond fast enough to 15k+ rpm.