There’s a lot of similarities and differences - the Steam Deck’s gaming mode is able to run a very barebones OS, similar to the very basic OS that the Nintendo Switch runs, with the game running in comparable sandboxes with stable software interfaces.
But Nintendo worked with Nvidia specifically to develop a variant of their hardware dedicated for gaming, while Valve essentially put a Linux laptop in a handheld console format (IIRC they did get help from AMD, but it wasn’t the same kind of deep collaboration), which notably may have different components between different hardware revisions.
When you try to maximize game performance that makes a difference, because on the Switch you can reliably push the hardware to the limits and expect it to keep working and on a Deck you have to test the hardware before pushing it. And if you find a trick that depends on architectural quirks you have to special-case it to not break on other hardware. There’s no guarantee that rarely used hardware features (both physical, and CPU/GPU instructions, etc) will stick around on a future revision of a Deck, while Nintendo guarantees forward compatibility (with help from Nvidia).
Nintendo even worked with Nvidia to emulate the Switch 1 GPU when running games for the first Switch on a Switch 2! They’re even going so far that they’re patching the emulation layer on a per-game basis to fix games where the default emulation method fails! And the ability to do this depends on knowing the exact properties of the hardware revisions of both the original and new GPU! (there’s architectural differences in the GPU that would break some games unless it was emulated)
Now Lenovo also has devices running SteamOS on different hardware, so games that runs on both either needs special cased optimizations for both, or only generic optimizations, or they simply have to decide to support one specific model better than others (which could end up with a game looking worse on better hardware because the dev didn’t try as hard with that hardware)
No, Wine (and Proton) is a compatibility layer (API translation, etc). Containers is an isolation method which hides the details of the OS from the software and gives it a standardized environment.
https://github.com/ValveSoftware/steam-runtime
No matter what Linux distribution you run Steam on, the only thing you need to do is to get the container system up and running. Once that runs, all software that runs in these containers will run on that device.