Seems fixed on master.  I don't know when exactly it was fixed, I was
running all that time with diff-update-on-the-fly set to nil.  But just
as I was writing a workaround patch (attached for history purposes, in
case it might be useful at some point, but right now it isn't), I
tested and it turns out both query-replace-regexp as well as delete-
matching-lines result in hunks being updated on the fly.

So bug has been fixed, the report can be closed.