Again, low profile can refer to either the switch (and the pcb's) physical dimensions, but is also used to describe some cases (regardless of what kind of switch).

So yes, low profile switches must match with a compatible low profile PCB, which you'd want to match with whatever case that pcb comes with. Based on your response I'm assuming you're actually talking about low profile switches like https://www.gateron.co/products/gateron-low-profile-mechanical-switch-set where the switches (and almost always the keycaps) are shorter.

Some cases are what some call low profile cases (aka floating cases) which is where the case's highest point (sometimes just the plate) ends mid-switch, so you can see the switch from the sides like https://www.gloriousgaming.com/products/gmmk-full-brown-switch.

Since I assume you're talking about a low profile switch build, I have not touched a low profile switch or looked up any new ones in the last ~5 years. They're relatively uncommon and seldom recommended. I don't think anyone can realistically tell you if you're going to feel discomfort swapping to a normal mechanical keyboard. I'd say in general people are willing to give up short term comfort and learn to get used to a different keyboard size because of the benefits of a full size switch keyboard. I don't know what kind of price point you're at or if you're even looking at custom keyboards, but choosing low profile will heavily limit your options.