Snap can install non-desktop applications just fine. I've only ever seen Flatpak for desktop apps, but I use snap for installing things like docker, lxd etc.
Isn't the entire point of snaps (and flatpaks?) technology that it's isolated? So the application won't be able to do whatever to your computer. But docker, lxd and similar usually requires root permissions to run, and access to bunch of sockets and what not.