Flatpak does have answers for this stuff but it's more the programs inside them aren't utilizing the right APIs, they are meant to use the portals api for filepickers which would use the system filepicker and securely portal stuff through the sandboxing. But many apps just don't.

Theme is also an odd one. GUI design in general has shifted away from an OS theme and more towards an app/product theme which stays consistent between the product on different platforms. Discord for example looks largely the same on Linux, Windows, iOS, and web.

Even for apps that don't use one of the native toolkits like GTK or Qt, where this has been a solved problem for decades, they should at least respond to a dark/light mode flag if they can. Flatpaks mostly don't.

They don't even have the same cursor as the system a lot of the time. It's especially cool when running display scaling when some apps shrink the cursor to a minuscule size too because of poor system integration.

I believe it doesn't work for me to open a directory of HTML files in Firefox: it just opens one file, and that's it, so style sheets and links are missed.

I've worked around by running a local web server for that content, but I'd rather if it just worked. The problem is also in some apps that open web browser for their documentation by invoking them directly.

If the apps inside need to be specifically coded for it, then why is it "marketed" as a way to sandbox currently existing apps?