The big difference for me was learning to use EQ to deal with room modes. In a sense, that is what you are doing when EQ-ing the sub, though there are two octaves above the sub that are also subject to room modes (80-160 and 160-320) so that is where having some more EQ in the system (like ARC) can make a big difference (similar to EQ ing the sub) and luckily ARC as well as most other good systems lets you choose to stop the EQ process at any frequency.
Toole has some great explanations of this in his book and in that lecture on youtube where he shows that most decent speakers' response is very similar below the transition frequency since you are mostly hearing the room, and it is above that realm (ie, c. 400hz and above, depending on room size) where the speakers tend to exert more influence than the room.
And, by the way, he also agrees with you that EQ above the room modes realm is a losing battle and does more harm than good in many, maybe most situations.