I do agree with your point, specially when it is not the first time a package maintained by that guy does non-expected behavior like https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1010165 (Inappropriate package, modifies other package's (conf) files, should be removed from archive).

I disagree that "modifying other packages' conf files" is a problem. Conf files in general are there for the user to modify, and as the maintainer points out, it shouldn't matter if the user uses vi, joe, emacs or this specific tool to modify them.

The problem in this case is that the package modifies generated files belonging to another package. Making it about conffiles is bad phrasing by the bug submitter.