Most derivations are pretty flexible; the ones that aren’t, however, will require you to write your own overlay to fix them. Or just fork them entirely. This is one of the advantages in Nix in that you can create reproducibility at any granularity. Writing and using your own derivation is complex though. Most packages provide more than enough knobs to change their configuration on their own in my experience though — my current Nix build uses no derivations I had to write myself.
Home Manager and Nix itself are versioned so I don’t understand your complaint about config changing. If you’re happy with how your system works just don’t update it to a newer version. If you do, as in any other software, you risk breakage. The advantage of Nix in this scenario obviously is that rolling back in the case of an upgrade going wrong is incredibly trivial.