I don't have the use-cases or time to test this feature myself. If you tell me that you or whitequark tested it and it works as you expect, I would be glad to merge it after code review. I would be slightly happier with a test for it in the ocamlbuild testsuite, but I won't make it a strong requirement.
(I'm rather thinking of "trunk only". Is anyone dead sure that this cannot break existing projects?)
I checked on an example that the -I flags were passed correctly.
I don't mind it being committed to trunk only, I was just looking at issues targeted 4.02.2 that could be fixed easily. It could potentially break exsiting projects as C stubs might be passed more -I options. Although it's quite rare for ocaml projects to install header files.