DEQ is supposed to boost the low frequencies only. At any specific spl/vol below reference level, the boost applied will drop progressively as frequency increases. As well, at a specific level and frequency, it will drop with increase in volume. So if the Atmos modules as mounted don't have much bass response to begin with, then DEQ will not have much effects on them. Again, these is all in theory, it is of course very possible that you don't prefer such LF compensating scheme, or Audyssey is simply not good enough, or both. As you must know, the old "loudness" schemes attempted to achieve the same goals, but I never liked/used that feature because I didn't find the effect natural. DEQ, to me has taken the "loudness" thing to a new level, to the point I find it indispensable, but I am sure there is a lot of room for improvement, though it looks like Audyssey has given up..
Attached are two of my very old graphs that show the effect of DEQ, note that by the time it reached about 120 Hz, the boost was only about 3.5 dB.