(Rhys -- I see you've fleshed it out quite a bit since we chatted in the CB.)
How 'bout having your perl app read the dir list from a config file? This not only lets you change you mind about the MIBDIR layout, but keeps the changes confined to the app's process tree and lets your end users choose different MIBs than yours, should they wish to extend your app.
In fact, with that, you could even keep your MIBs completely out of the common hierarchy.
Remember, when you stare long into the abyss, you could have been home eating ice cream.