I think that’s a bit harsh. Many times I have faced that prompt during an upgrade (not on the Librem 5, this is on Linux generally). The reality is that in practice it may be that both options (keep the existing file, take the package maintainer’s file) will break the system. Usually the only way forward is to save all the versions and, after the upgrade, carefully study all the changes, and the documentation, to work out what is needed.
Given the pace of development on the Librem 5 (i.e. lots of things happening), a user should probably have a bias towards “take the package maintainer’s file” and sort things out afterwards - and a bias against getting too creative with local configuration at all. Just my opinion of course.