Rotated switches could be a problem, but that really depends on the specific cap and switch:
I have some brand new mx clear switches that are already dam stiff as is to get caps in, and once you get them in, they're extremely hard to get off. Now if these same switches are rotated, it will be near impossible to get them on. If you do happen to get them on, I don't see how you're going to get them off without ripping the whole switch off the PCB/plate, along with some traces. Some stems are extremely tight even when not rotated, some batches aren't. The point is that not all are made equally.
Now as for caps, the tolerances will also vary between different caps. Some are really tight and will be nearly impossible to even get it on a rotated switch, but most should work. If you do happen to get it on, some will retain the grip pretty well, and some will be permanently loose. For example, imsto's caps are thick PBT caps, but ironically they are the loosest caps I have after only 1 or 2 installations. If you even think about turning them sideways and mount it, they will become looser than a women that just had 10 fat children.
So it really depends on what switches and caps you have, and if you'll be transferring the cap sets between different keyboards. I personally don't care, but would rather bring this up for people that do care about this aspect.