Just like many people, I've customized qmail/vpopmail quite heavily. It lends itself to customization really well. Now, with the changeover from Maildir to .maildir, I forgot that I had a few scripts that use safecat to inject mail directly in the users' Maildir, now .maildir folders.
For the old maildirs, the upgrade script created symlinks, so you the existing scripts continued to work alright. New users, however, started losing mail and started complaining. Eventually I found the Maildir references in my scripts.
To cut a long story short, what's actually the added value of arbitrarily changing Maildir to .maildir (who the hell cares)? I mean, does the supposedly added value of this change exceed all the unneeded trouble that it creates? Could the people here in charge of vpopmail/qmail please stop tinkering with it and please leave it alone? It's a brilliant piece of software, and I don't need unnecessary changes, thank you.
Steps to Reproduce:
every maildir system on gentoo was already using .maildir, and the fact that vpopmail was still using Maildir was breaking courier-imap amongst other things.
The entire point of my modifications to qmail/vpopmail with new config files was making it much easier for people to set up and maintain thier customizations across versions of qmail/vpopmail.
if you really want to stick to 'Maildir' just copy the ebuilds to your local portage overlay and modify them (very small change to do it).