RouterOS detects common P2P protocols, not all. It is not possible to detect traffic that is encrypted (you can only drop encrypted torrent traffic, when bittorent is denied at your router).
There are no difference, if you are using 'queue simple, then mangle rule configuration for marking p2p is not required.
initial ip packets of encrypted p2p connection can be recognized, and therefore can be dropped and connection will not happen, with encrypted traffic - it is encrypted and completely undetectable for limiting.
but if you set queue for user, then he will be limited to that amount of traffic no matter what kind it is.