You point out the inherent flaw in these room correction technologies in that they tend to stifle the bass too much especially at the low end. If you check around for info on this site you will find "somewhere"(I can't quite remember) a video from "President" Ian discussing this very issue in that microphones and also meters like the one from Radio Shack do not read bass response accurately below about 50hz. There is also a blurb about this in one of "Outlaw Audio's" manuals for one of their subs in which they talk about much of the same problem in that bass must be boosted manually at certain levels to compensate for this loss, hence, the problem you are discussing.
Although not everyone is in agreement about this, I would recommend something like the Velodyne SMS-1, the new Audyssey Bass management system or anything else that enables one to "fine tune" the overly reduced frequencies at the low end, that is, of course, if your sub can handle the boost.
In the end, it is always about what sounds good to you.