I really dislike this proposal as it stands. While I'm fine with a position that says "for normal users, don't have Makefile.in depend on Makefile.am", I *want* that rule as a package developer and even as a release engineer.
I already have way too much stuff I have to remember to do, and adding an extra step to make sure that generated files are up-to-date is just asking for more work and problems. Put another way, if somebody want to have sufficient mechanism to allow these behaviors as choices, and if somebody wants to have a way to specify that strict GNU coding policy can be used that's fine with me. Just be sure to make it trivial enough that I can override that policy choice locally so I can work more efficiently. H