This is true for essentially all Win32 programs too, including the ones that have started to appear in the MS Store. Developers can play in the sandbox from the get go by using Windows Runtime, but no one wants to rewrite their application with a library or environment that Microsoft is going to deprecate and replace in 6 months time.

It's not like Flatpak is perfect, but at least it uses primitives that we understand through containers, and can apply to already existing programs. Even though they were written without playing in the sandbox and might expect full access to services and files, we can fudge it for the most part with bind mounts and open up safer doors through Portal and widget toolkits over time.

I haven't used Windows in a long time, but IIRC Windows behaves the same way. At least, on Linux, there is an expectation that user accounts be actively used, and this is indeed the model followed by most critical software like nginx, postfix, dovecot, etc.