The problem I had with flatpak and the immutable approach in general is that I can't modify them in ways that aren't supported by the developer. For example, I use decsync to sync my calandars but as far as I can tell, it's impossible to add the decsync plugin to the evolution flatpak. Until these immutable systems support the stacking of custom overlay filesystems as a first class feature^1, people will continue to…
NixOS gives you precisely this kind of control- through a few different mechanisms. Some packages in nixpkgs, and most NixOS and home manager modules, expose a lot of configuration options where you can configure various plugins, add extra packages, etc. Nix also lets you provide overlays and overrides to add custom packages (new packages, or customized versions of existing packages) and gives you the option of changing parts of a package. If none of that is sufficient, you can even supply your own patches to the code, or build the package from your own fork of the upstream repository.
In practice this is one of my favorite things about nix. I find that I contribute much more to open source in general because it’s so easy to say “replace this dependency with my version when you build this package”.