No idea if libgit2 provides any kind of support ATM, but would be nice to
have better diffs with hunk headers.

See http://stackoverflow.com/questions/28111035.

Just to be clear, the request is for improving the current header or for
offering to projects the possibility to set their own header?

The first one seems reasonable (but here as well, I do not know git pygit2
offers it), for the later one, I am not convinced.

Just the former, using either some default heuristics like in stock git,
or at least the first line without whitespaces at the beginning that is
above that hunk might be enough for most of the uses (C + derivates,
Python, Ruby, ...).

I found something related to the hunks in pygit2: http://git.kaarsemaker.net/pygit2/commit/11d0c9a30f0a2d5e2510acbf5671a9b6df2eff1f/
but when I try to make use of it, the value seems to be empty... :(

The last update was 7 years ago, no further requests, updates or actionable tasks since then, I'm going to close this issue for now to reduce our backlog.