The characters can wear underpants over pants, Superman style. For underpants this is no big deal, but then there are hoodies, backpacks, holsters etc.
There is no penalty for this behavior. You can acquire a gun through pants (regular holster, not some holdout variant), sneak a whole full duffel bag (two, no FOUR duffel bags!) inside a hazmat suit, wear a t-shirt over plate armor.
The problem, apart from the obvious muh realism stuff, is that it is optimal to shuffle around gear to keep stuff from getting damaged. This can get tedious early on, before you craft a whole set of indestructible armor.