While it is indeed linux, the core file system is locked down and cannot be accessed without running a bunch of commands. That isn’t recommended either, mainly because steam deck updates will lock the file system down again, and you risk breaking your system. Because of that, the only kinds of applications you can run are flatpaks, which are installed in the user’s home directory and are sandboxed. You can install such apps via the discover app.

If the app you want to run doesn’t offer a flatpak version or an appimage (which is essentially the same thing as a portable .exe file on windows), then you are out of luck.

When it comes to android apps, normal linux does not support them natively. First of all, android runs on an entirely different CPU architecture called ARM, so it needs to be translated to x86 first. Second of all, the kind of linux that runs on android is heavily modified and afaik isn’t the same thing as normal linux, so there may be some translation going on as well.

If you want to run android apps on linux, you will need to use an app called waydroid, which does all of this for you (the ARM translation is done by libhoudini, which you will need to install manually, but it shouldn’t be too hard). Unfortunately I don’t think they offer a flatpak version.

Furthermore, waydroid runs on a rendering method called wayland, which I’m not sure is turned on in the steam deck’s desktop by default, so you will need to figure that out. Most people still use the older rendering method called X11 on other linux distros.

The UI you boot into, called gamescope, uses wayland by default so you should be fine there, but I’m not sure about the desktop session.

Tbh I don’t think running android apps is worth it on the steam deck. It was a major pain in the ass for me on Fedora 38 to set up, didn’t work for the game I wanted due to anticheat and who knows how the controllers work there. I couldn’t figure out how to bind keyboard keys to specific screen locations, so I assume controllers are going to be even worse.