You should read the REL 212/SE review in The Absolute Sound. It details the integration of a pair of 212/SEs in a large room with large full range speakers.
As you are discovering, you have a very large acoustic space because you have large openings to other rooms you cannot close off. The effect of this is heard mostly in bass frequencies. Your ears are not as sensitive to bass and extreme high frequencies because they are tuned to midrange frequencies, think the human voice. This is the science behind a loudness curve. As you listen at more real life volumes the bass can get out of balance, so make sure and use your regular listening levels during setup.
I can tell by your comments and commitment to this effort that you are what some would call a bass hound. I am also. I have had the great privilege of experiencing many reference quality systems in my life, despite never being able to afford equipment of that level. I used to sell and install high end stereo and theatre systems before changing careers in the 90’s. I worked at a retailer that made the investment to have high quality systems in the store, so customers could hear them. I also set systems up in homes and experience the results first hand.
The popularization of home theater and the vast improvements in subwoofer technology have brought good quality bass reproduction to the masses. It is easy to get enough acoustic output today. It is still very difficult to get high quality bass reproduction, as you are finding out.
I frequently took great pleasure in allowing customers to experience sound better than they wanted to afford. The expression on someone’s face when they heard a favorite song on a really good system was priceless. We had a pair of Infinity IRS Beta speakers set up for demo. They were an example of what most folks would call overkill.
When they heard them, they frequently commented on the lack of boom in the bass frequencies. They were hearing, for the first time, what having enough subwoofer meant in a system. You seem to be getting there also.
Let me caution you about getting too tied up with getting flat frequency response when integrating a small set of monitor type speakers with subwoofers in a large room, you will drive yourself crazy. Use the equipment for initial setup or to solve a boom issue as you seem to have. Use your ears, they are the best test instrument you have. Everybody has a different perfect sound. You might find that ultimate flat response is too much bass for your taste, this would not be unusual.
Having enough subwoofer should result in you not noticing them as much. Paul McGowan has said, mid bass, the point between a sub and midrange , might be the most important part, and hardest, part of the system to achieve. This system synergy is what makes subwoofers disappear.
If you ever get the chance make a trip to PS Audio when they get the IRS Vs set up in the new building. I had the privilege of hearing them last summer, and they were magical. It brought back the memories of all the great systems I have experienced.