If you are doing it only to address a few cracks, I would say it's probably easier just to address them and paint
normally (or patch the gelcoat, depending on overall condition). You'd want to do some work on the cracks even for the rougher paint
On the other hand, if you like the texture of the truck bed liner, and want to do it anyway, well then of course it will hide a certain number of small flaws.
I think it looks kind of neat, but I don't think I would want it myself because (I think) it might be hard to clean and keep clean.