@Wolf64 As I mentioned in my previous post, I am not familiar with lr-stella. I've never used it. That is why I asked in my post, "are all these mappable to a controller in lr-stella?"
I only use the standalone version.
For sure the keyboard works in the standalone version because I do it all the time.
I've never attempted to map these functions to a controller button in the standalone version. I've no reason to try this as I only use real Atari joysticks, paddles, driving controller, etc.
I don't have a different controller to test the standalone version for you, sorry.
Maybe the developers here that modded Stella for RetroPie can chime in and confirm for you.