Here's a patch which partially addresses the issue. This will allow for cross-sub-project patches to apply cleanly, and will comment with a "-0 patch..." in the JIRA comment if this is detected. It won't actually run all of the tests from all affected modules. Since that's a substantially more involved change, and since this change should help considerably, I'd like to punt that to a separate JIRA.
I tested this patch by creating a few uni-project and multi-project patches, and running test-patch manually. With this change, test-patch successfully applies and detects cross-sub-project patches.