some Makefiles use indents or var placement as semantic cues. if a tool rewrites them mechanically, it might clean things while killing meaning. is structural correctness enough, or do we need formatters that preserve human context too?

Ideally, we'd have linters that preserve the human context as well. But human context may be too ambiguous and high variance enough that it can be impractical.

It's hard to say what's intent and what not, maybe linters with many custom rules would work best.

That doesn't sound any different than it is for any other programming language, but many people prefer automatic formatting anyways.