Adding a git worktree is a great way to being able to change the version history without changing all the other files under /etc to some arbitrary old version while doing interactive rebases etc. With a worktree you can do all the work there and then merge in the final result in a clean operation in /etc later on.
This could be done by cloning the repository and add it as a remote instead, but that is more cumbersome.
However the pre-commit hook messes things up when it is being run inside the linked worktree as well. It really should only run in the main worktree.
Could you please merge the worktree branch which contains one commit that adds a check to avoid running the pre-commit hook in linked worktrees?