Well, the main problem has been solved.
User error was the problem, (as expected). The thing that broke the dam was figuring out that the input_..._btn entries were for the controls vs. input_...(no _btn) entries. When I looked closer, I figured out I didn't have a complete set of hotkey inputs for the keyboard or the controller in the .../all/retroarch.cfg file.
So that is sorted. I still would like to know the answers to the other questions, but I can live with this.
Thanks!