The file-in-the-repo argument is strong and I do not have a good answer to it. Version-controlled, visible, and stale entries show up in a diff instead of needing a monthly audit - that removes the exact failure mode I wrote the post about.
The honest counter is only that it does not cover the cross-project preferences, which for me is a short list of output-shape and anti-preference entries. Which is roughly what everyone here has converged on anyway: a handful of negatives, nothing about the current state, nothing about me.