Makes sense, I wasn't altogether happy with the complexification. But we're leaving the user high and dry when tracking down errors.
Take 4.x and just copy collection1 to collection2 and fire up solr. No warnings in the log. No errors in the log. But you can't get to collection2, you get a 404 error. And any index mods are done in the collection2 directory.
Admittedly the configuration is foo'd and Solr is doing exactly what the defined behavior is (identically named cores last one wins). But how the hell is someone supposed to track that down? Especially with lots of cores? They don't get a single clue in the place we always say to look, the solr log.
I see where there are tests for creating a core with the same name as an existing core via the core admin handler, but I don't see at a glance any coverage for this scenario.