Definition of LFE:
The low-frequency effects (LFE) channel is the name of an audio track specifically intended for deep, low-pitched sounds ranging from 3-120 Hz. This track is normally sent to a speaker that is specially designed for low-pitched sounds called the subwoofer.
If you aggressively high pass filtered the signal to your mains at 40Hz or so, that might work, but HT LFE content can be stupid loud and low from a music standpoint. For example, the powerful strikes of the tympani of Also Sprach Zarathustra (Theme to 2001: A Space Odyssey) is no lower than 60Hz. I'm betting your towers would be phenomenal with these drums at a spirited volume!
But if you feed them the LFE from "Lord of the Rings" at an engaging volume level, you will push them beyond their limits.
This begs the question of whether Ed's main concern was sending LFE content to the Ultras or if it was isolating the woofer section and applying miniDSP to it.
So, I think it'd be reasonable to use them full range and manage the bass using the miniDSP (but without adding the LFE signal). I would be slow to do much with miniDSP in the higher frequencies and let Audyssey manage that, but in the lower frequencies, it makes sense that your towers are having the normal issues of low frequency room effects. Whether you isolate the woofer section or simply apply miniDSP to the lower frequencies doesn't seem like it'd matter much, but I like the idea of knowing you cannot impact the higher frequencies after you separate them.
From what I've read, the low end of those towers is very nice and it seems a crime to cross them at 100HZ (IIRC). It also makes sense that room modes beyond what Audyssey can easily handle may be the reason that your curves look best when the towers are crossed so high.
I would be tempted to start fresh, tuning your system without the subs and with the woofer sections on the miniDSP, just to see how good you can get the towers to sound (with music) and what you learn from it!
Actually, I just found an old (2012) article that does a great job of discussing much of what you are doing/considering!
https://www.soundandvision.com/content/schroeder-frequency-show-and-tell-part-1
From part two:
Any tower speaker ... with speaker-cable binding posts that allow the bass section to be separately amplified, can be optimized for smooth bass response in your listening chair even if the speakers are placed for the best midrange/treble performance. All you have to do is connect a low-frequency equalizer such as the Velodyne
SMS-1 or the
MiniDSP, then dial in the EQ for flat bass response.
Edit: I was piddling around and had this post sitting on a back burner for several hours. I am not posting this as a direct contradiction of PENG's (or LovinHD's) posts (which I did not read until after I posted this). I am more throwing out food for thought ... I don't know enough about this to argue what you should do!