Updated:

The option to configure the controller from a "desktop library context menu" doesn't exist on Linux either.

Another update: Okay so editing the config does work, but there definately isn't a way to get the desktop client to launch with big picture overlay as the changelog says on Linux.

You have to have a Steam controller active for the config editor option to be present, but the overlay option is disabled right now on Mac and Linux due to focus tracking bugs in SDL preventing it from working properly. This was originally specified in the beta release notes, but got lost in translation, sorry for the mixup.

I see, any word on when those might be looked into?

Is this still the case? I still can't get the controller overlay to work at least (even though the regular overlay works fine).

This is still the case. To get the Big Picture Mode overlay on Linux, you need to use BPM for now.

Thanks, knowing that i can get it from BPM is helpful. At least i don't have to quite the game to configure the controller constantly like this.

The global setting now works, the overlay is functional; however input for controllers is broken in every game I've tested. Haptic feedback is missing, so configurations aren't loading properly. Probably the same issue as https://github.com/ValveSoftware/steam-for-linux/issues/6495

Works for me now, though it took a moment to find the setting. It looks like there is no way to set it per-game, it is just enabled automatically at launch if you have the Steam setting enabled and the game is using Steam Input while a Steam Input configured controller is detected (or something like that).