This sounds like a dream setup, higher sub xover to reduce IMD, and digital xover at 2.1 KHz should help with any physical xover artifacts.
My listening space doubles up as a home theatre, thus I will limit myself to SW EQ for the 2 channel solution, AVR sub integration, and no EQ for home cinema other than what the AVR can do natively.
Was the sub placed close to the speakers or closer to the listening position?
If you had JRiver and Dirac Live and a software based crossover, you could do what JRiver call separate zones for each use case (2.1 stereo and multi channel home theater with the sub used for LFE.) You would just use a different crossover and sub tuning for each use case, and Jriver could even do that automatically by switching zones based on the decision rules you give it for which zone to make active.
This will be one of my projects when all the hardware I've already paid for finally arrives at my door. I'll probably be adding a second (used hopefully) SB 2000 and bumping the xover up to 150hz at that point.
Finally, Dirac has a multi bass management module which is supposed to be major improvement for integrating subs and mains, and it includes a crossover as well, so at that point, JRiver + Dirac Live 3 with multi channel base mgt should become my ultimate solution,.
And the electronics and software on the system are such that they could remain at the heart of any stereo/home theater system regardless of cost. If at some point I get more room for my hobby and decide I want a pair of F328be's or a Reference 5 by Kef, this system could easily power it and my 4 Ls 50's coud be employed for surround duty.