Summary for anyone trying to follow this thread:
Looks like retropie 4.3 defaulted to atart800 emulator. This needs a keyboard so I eventually found a hacked version of such to remap L&R shoulder to start/select to make it usable with just controller
retropie 4.4 seems to default new installs to lr-atari800 which has similar keyboard required, and doesn't seem to be able to change much via its config files. Actually it looks like to ignores just about anything given to it and there is no useful way to alter its behavior with command-line arguments. It will accept some retro arch config changes if done through the GUI console.
future.child lead me on to kat5200 emulator which an install script is available, This will download, compile, and install the kat5200 emulator into retropie.
The kat5200 emulator needs to be set up via keyboard, but once done so seems to work quite well. You will need to configure the location for your BIOS files, and then also define your input source (joystick) and re-map buttons where needed. The input screen can do most key mapping, and the user config screen has the exit emulator sequence. Two step button sequences can be set, so the usual select-start emulator exit can be emulated. Tip: seem like the config works better when you define multi press sequences in reverse, so when setting up the user input exit function, define 'start' as the first key then 'select' as the second. For my setup, I mapped #1 key to joypad-1 left soulder, #2 key to joypad-2 left shoulder, this works for some games to select 1 or 2 player. I also mapped # and * keys to X & Y on each controller as I think those are needed in some games.
I haven't tried anything beyond Atari 5200 games with this setup, but for that it seems to work well for a good selection of 5200 games.
I hope this helps someone!
