Jeff King [off-list ref] writes:
But I have not thought hard about it, so maybe there is a good reason
not to (it is a little weird just because the resulting index is a
partial application of the patch).
Originally ".rej" was a deliberate attempt to be "not very Git but
more like 'patch'", so I wouldn't be surprised if the combination
between "--reject" and "--index" did not work, in the sense that we
did not add such a partial change to the index.
I do not offhand think of a reason to forbid the combination,
though, as long as we make sure that "git apply --index --reject"
still exits with failure to prevent a partial application to be
auto-committed.