A (sad?) state of Nixpkgs

That one is easily override-able:

nautilus = pkgs.nautilus.override {
  gnome-user-share = null;
};

I too support the concept of maintaining such flags, and I try to do my best in some of my own packages were these flags are meaningful in my opinion. However, indeed that can become hard for some packages, so in your case I can only recommend to you to try to fix those issues yourself:).

Also relevant:

Given such a module system laid out in Nixpkgs, it would be interesting to explore the automation of testing combinations of such flags via a passthru.tests by using lib.mapCartesianProduct.

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