I'm not very invested in finding flaws in your workflow, but I am happy it works for you. It does sound interesting and I'd honestly like to know more about how you have it setup.
I stopped using desktop Linux a long time ago and now use a Mac for my desktop work. I take things a bit further and don't let anything write to my $HOME/Desktop -- it's read-only. I don't recommend that as a default for anyone either!
But as far as Flatpak, a few of the "featured" apps are things like Inkscape, Gimp, VLC, or LibreOffice. Not apps that you'd really want to sandbox isolate like you described. (And as you mentioned -- you wouldn't want to do that anyway).
Now a few of the others were Spotify and Slack. Things that you could (should?) definitely sandbox.
I guess I don't see the point in having applications (that is intended for a general purpose user) that (a) need access to your home directory to read/write files and (b) should only have access to a sandboxed pseudo-home directory. Either sandbox it so it doesn't have $HOME access at all, or don't. I'm not sure I see the benefit to this middle ground. Especially for the use-case of general user desktop applications. For server applications, I could potentially see the benefit (although, containers have probably already filled this scenario). What is the use-case you're thinking of?
I appreciate your point of view that no one should be able to decided for you how to sandbox software, but no one is forcing you to use Flatpak packaged programs[1]. Perhaps there should be some way to re-build a Manifest that limits access, or make it so that you can more easily switch granted privileges -- that would probably be a good thing. But someone has to set defaults. If a Flatpak packaged program has too liberal defaults, then maybe that's best treated like a bug and hopefully there is a mechanism to send a patch.
[1] yet... but it might be coming. I think the only way you'd see commercial applications like Photoshop for desktop Linux would be wrapped in something like Flatpak. I still think that most open-source applications will still be packaged by the main distro repositories, regardless of how well Flatpak does.
I stopped using desktop Linux a long time ago and now use a Mac for my desktop work. I take things a bit further and don't let anything write to my $HOME/Desktop -- it's read-only. I don't recommend that as a default for anyone either!
But as far as Flatpak, a few of the "featured" apps are things like Inkscape, Gimp, VLC, or LibreOffice. Not apps that you'd really want to sandbox isolate like you described. (And as you mentioned -- you wouldn't want to do that anyway).
Now a few of the others were Spotify and Slack. Things that you could (should?) definitely sandbox.
I guess I don't see the point in having applications (that is intended for a general purpose user) that (a) need access to your home directory to read/write files and (b) should only have access to a sandboxed pseudo-home directory. Either sandbox it so it doesn't have $HOME access at all, or don't. I'm not sure I see the benefit to this middle ground. Especially for the use-case of general user desktop applications. For server applications, I could potentially see the benefit (although, containers have probably already filled this scenario). What is the use-case you're thinking of?
I appreciate your point of view that no one should be able to decided for you how to sandbox software, but no one is forcing you to use Flatpak packaged programs[1]. Perhaps there should be some way to re-build a Manifest that limits access, or make it so that you can more easily switch granted privileges -- that would probably be a good thing. But someone has to set defaults. If a Flatpak packaged program has too liberal defaults, then maybe that's best treated like a bug and hopefully there is a mechanism to send a patch.
[1] yet... but it might be coming. I think the only way you'd see commercial applications like Photoshop for desktop Linux would be wrapped in something like Flatpak. I still think that most open-source applications will still be packaged by the main distro repositories, regardless of how well Flatpak does.