Yeah I've read up a lot on how full range room correction can do more harm than good, specifically for the reasons you mention as far as eq'ing the combination of all direct and reflected sound, which does/may/can make things worse even if the measured response "looks" better on paper. For this reason, I have chosen to limit eq in my room to below 600 Hz. Although below Schroeder is often regarded as ideal, my response is quite a wreck up to 6-800 Hz so I decided to run a little higher. Above that point, measured response looks reasonably good in my room. Much more so with my current speakers than with my last couple of pairs.
This is a lazy weekend....thought about breaking out REW to measure a bit more, but that's as far as I've gotten. Might be changing subs in a couple weeks so it makes sense to wait until then to play. As I feel like it might garner some interest, I'd like to create a thread regarding subs, eq, integration with speakers, measurements, and maybe some comparisons between my current subs and the ones I'll be switching to, including compression sweeps and distortion comparison. I think I will lose 6 dB or so in the swap.
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For example, perhaps run sweeps on the L,C, and R raw without eq. Then with eq below my cutoff frequency. Same with subs. Raw response, after eq, and blended with speakers to show full range response. So time consuming though.
I'm also interested in looking at distortion from the speakers on compression sweeps without eq, then see how eq affects distortion/headroom.