My understanding of the migrations folder is for when a user wants to use truffle migrations as well as ZeppelinOS. This could be where a user has a mixed project of upgradeable contracts deployed using ZeppelinOS and non-upgradeable contracts deployed using Truffle migrations.
There was a discussion recently on how to manage non-upgradeable projects in ZeppelinOS:
Also information about minimal proxies support in ZeppelinOS in the May development update: