That is NOT a problem. Because which is an external program, it can't know about things like shell aliases and functions, and that's OK because users know it or expect it. Indeed, if you're writing a script then you already know what aliases and functions are in it, and you're only going to be interested in knowing what's outside the script -- which(1) does that just fine.

Stop looking for problems to solve where there are no problems. It's a waste of others' time, not just your own. Be respectful of others' time.