So not to keep beating a dead bush, but the aforementioned solution doesn't actually work.
If the project is cleaned, and then the gradle script objects are compiled some time later: (ie gradle clean, gradle generateDebugJavadoc as opposed to gradle clean generateReleaseJavadoc) they'll never find the intended classes.jar files (because they don't exist in the project yet).
What I ended up doing was creating a different configurations container for aar files, and extending compile from it. This allowed me simply to have a set of exclusively aar dependencies, which I could then strip the groupId, artifactId, and the version from to manufacture the expected path to the classes.jar in buildDir/exploded-aar/.
This is not ideal, but it works.
I'd be glad to hear if anyone had any better idea.