.INBOX is actually a folder, and .INBOX.whatever is the .whatever folder under the INBOX rather than as a folder under their user account. I'm not explaining this well, so a picture....
Code:
Myname@domain.com
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+-Foldername <- This would be .Foldername
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++-INBOX <- This is .INBOX
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++-Foldername <- This is .INBOX.Foldername
|+--SubFoldername <- This is .INBOX.Foldername.SubFoldername
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If you do your rename that you suggest this will flatten and move all the folders people have in their INBOX to outside their INBOX, and will probably break any rules in place.