You didn't do anything wrong. You asked for opinions from the Ayre community and got responses from others as well. Ayre is designed so that best results are gotten from a system that is time and phase correct. Most people think that's an issue for speakers, and it is. However, its important that the signal reaches the speakers as "untouched", as possible. That's why Ayre, starting from the source, uses balanced connections and 0 feedback all the way too, and including the amp. When you start in with xovers, phase is altered, There may be other adverse effects, but that will depend on what you are putting in the system. With most brands, you probably won't hear anything out of the ordinary, but Ayre is very detailed and sensitive to these types of distortions. I can't speak for anyone else, but anytime I've experimented with different typs of components and designs, I can clearly hear the differences.
"The problem is with what I hear below 100 Hz using the LS50s. I'd like
to remove those frequencies from their duty. And to do that seems to
require intervention between the preamp and amp."
That's why you should use full range speakers with subs. Regardless, there's a better way to do it. You may have noticed that some subs have speaker cable terminals. Use those instead. You run speaker cables from the back of the power amp to the input on the subs. This type of connection has no effect on your amp because you are using the speaker cable at IC's. No real power goes through them. If you are looking for a music solution, connecting a sub this way is prefered. For something crude like HT, it doesn't really matter. For music, if you don't get it exactly right, you won't be able to listen to it. After a few days you'll just unplug the subs and go without.
In my listening room, I have 2 Ayre V-5's and 2 subs connected in the above manner. I wouldn't tell you to do anything that I wouldn't do in my own system. I would ask, though, that you not take my word for this. Call Ayre and ask him if this setup is a better option. That way you have the piece of mind that comes from Ayres approval, and not go by what some stranger on the internet told you to do.