I have wondered about whether built in speakers work better but what I've noticed is that even small changes can make noticable improvements. Using these speakers requires time to get the setup right. So you might think that your up-firing speakers are working at optimum when they are not. This at least is my personal experience.I have both setups, up firing PSB modules in our living room & ceiling speakers in the home theatre.
From my own experience, ceiling speakers are better than upfiring modules for Atmos.
My living room has a good reflective surface and the effect in noticeable, but isn’t a patch on proper over head speakers (in my setup).
If you had both systems in one room then that would do more do convince me of fixed speakers being possibly "significantly" better. Not to change my setup, that's impossible at the moment. Just that if the opportunity arose, there might be a future upgrade path.
At the moment I can't imagine Atmos sounding much better than it does, but then I think that has to do a lot of with how well Audyssey works in my room.