Minion will do its best and try to detect all the AddOns you have installed. If you have some AddOns not available on WoWInterface it won't detect those. If you find an AddOn is missing from the installed list after you install Minion you can always click on the "find more" tab, search for the AddOn thats missing and re-install it.
If you have any other questions please feel free to post them.
I moved your thread to the Minion forum 