For compiling the firmware from the M5-PbHUB-Internal-FW repo, try using the Arduino IDE or PlatformIO. Both are open-source and offer a more modern experience. You can also use the command line with PlatformIO, which is pretty flexible.
I do not have an M5AtomS3 Lite. But I tried the button example with an M5AtomS3 (which uses the same GPIO41 for the button) and it works for me. Care to share the code you tried where BtnA did not work?