I've been having the same issue. I have a MacBook Air M1, and after I updated to the 1.5.5 version, the Steam Overlay doesn't show up. Also, when I try to plug in a PS4 controller, it doesn't work in Stardew Valley, but it does work in Steam and in other Steam games.
I've checked to make sure that none of my firewalls are blocking Stardew Valley or Steam, and I've checked that the Steam Overlay is enabled and that Steam input is enabled. I've also tried going into Stardew's settings to force the gamepad input on, but it still doesn't receive input from the controller.