1. Do you think dual sealed subs would integrate well with the Encores in this configuration given the space limitation?
A sealed servo sub will work great.
And yes, while open baffle is awesome, and kind of the hill around here, you don't have the space for it.
2. Do you agree that the built in 80hz crossover on the A370PEQ should not be used?
Again, don't use that. It is not a high quality cap.
3. If so do you agree that an in-line passive capacitor would be helpful in filtering some of the low-end out of the mains and would this improve sound quality?
Yes. Here is an example of one with a by-pass for the servo sub.
I would go with a .1uF for your amp. That will get you a -3db of 72Hz and allow a crossover somewhere in the 60Hz range or lower. that will be more ideal with these speakers.
4. Do you think one Schiit Aegir will be powerful enough to run the Encores (max 20W per channel into 8 ohms) or should I consider switching to something like the Vidar with more power? Or is there another power amp that you personally recommend for the encores?
It may be fine if you are not far away from them and you don't clip it on them.
5. Do you agree that a 4-pin speakon connection would be a good choice to connect the sub driver to the amp if it's in an external enclosure?
Yes, we use them for that all the time and stock them for it.
We just don't use that type of connector for anything above 200Hz.