Okay, installed everything from a fresh RetroPie 4.1 image and also clean install of AM from source. I'm on version 2.2.0 of AM and everything is working as expected. The ghosted keys are no longer an issue, and as a result I don't need to futz with different key settings for exiting a game in retroarch. I'd like to figure out why that was an issue for me, but for now what I have is working. In windows I programmed the "exit" buttons for my minipacs with the WinIPac program to be macros of "start+select" and it works perfectly.
As a side note, it seems the issue was with sfml-pi. This explains why my 2.2.0 AM was still giving me issues. I had not gone back all the way in the steps to the sfml-pi portion.
Thanks all.