Handling version numbers in per-target runtime directories is another instance of issues related to the strict triple matching done by the new layout right now; I haven’t had time to implement a check for that yet.
In general, the per-triple layout is really nice in theory, but you run into all sorts of issues with matching against the triple in practice, and like others have said, I’d be opposed to removing the old layout until we have all the issues with the new layout sorted.