In some cases it's not so smart to put the CI flow inside the source code repository.

I got that point in case that I should release a CI flow update to 380 git repositories that doing the same flow (When I say flow I mean to Jenkinsfile)

So my suggestion is to give an option (in project configuration) to put a link for central Jenkinsfile and all branches will work with that

one more thing to think about is CI for multi-repo architecture