I was very disappointed to learn of the current situation with controller support on macOS 11 (Big Sur), which is apparently that Steam's controller drivers use some outdated methodology that Apple has blocked from installing on the latest version, so controllers won't work at all in-game, despite navigating Big Picture Mode just fine. Seeing this, I did some searching around online, but only found workarounds for non-M1 Macs, and/or ones that require tinkering with a bunch of technical stuff and disabling security features on your computer. Here is a solution that is easily accomplished in seconds via the Steam interface, and which immediately restored full in-game functionality in Hades using a PS4 controller (note that I have not tested other games or controllers). All you have to do is:

-Right-click the game in your library and select Properties

-Under the General tab, uncheck "Enable the Steam Overlay while in-game"

-Under the Controller tab, set the override to "Disable Steam input"

And done. I assume one these options are disabled, the built-in macOS controller support takes over, so obviously you can't use custom Steam button configs etc. Once again, I've only tested this with Hades, using a PS4 controller, on an M1 Macbook Air, so your results may vary. Hope this helps!