Given that we have the following repo structure:
<General Build Repo>

And we call the build in <general build repo> so the warnings paths are relative to <general build repo>, git blame doesn't work because the blame information is in <submoduleProject>.

A possible solution would be to do an aequivalent to the following:
Instead of: "git blame <submoduleProject>/path/to/file"
do: "cd <submoduleProject>/path/to ; git blame file"

That way the correct would always be selected to retrieve the blame info (a minor performance hit is possible).