Speaking as an FX mixer who has worked in three rooms extensively (uncountable rooms occasionally) that started as 5.1 and became Atmos; the major reason that some rooms are less than ideal in their Atmos implementation (home Atmos, not theatrical Atmos), is because the room's guts were built before anyone considered sticking speakers in the ceiling. You have hardware up there to avoid, baffles, HVAC, lighting, sprinklers, etc that require positioning around. Then you have to select a speaker that actually works within the envelop of the positions you have and is voiced somewhat similarly to your main array (not impossible but not trivial).
Lastly you have to consider not just the intentions of Dolby but also the intentions of the room and the film maker. There are several instances where I've been in a room that Dolby measured as "acceptable" but a huge amount of potential acoustic energy was behind the MLP (sides slightly behind, rears behind, rear tops behind). This doesn't make a lot of sense because it means that that the soundscape will have a tendency to sound biased to the opposite end of the room that the screen is in.