Indeed, you're right. Just like any other soundtrack that may have, say, non-aggressive surround channels in the mix to begin with, the Atmos channels could be quiet either by design or by engineer/mastering error.
But here's the thing, in a nutshell: If I am running in-ceiling speakers for surrounds right now, placed over our listening positions, would Atmos even make much of a difference? As it stands, when we watch Blu-rays and Ultra HD Blu-rays that contain Atmos mixes, these are "dumbed down" on our system to their core Dolby TrueHD signals (in our case, in a 5.1 arrangement) and we get plenty of "overhead" activity from those ceiling speakers...so would Atmos modules even make sense here?