MIB definitely recognizes the boy which means he is NOT Aaron. Why would he recognize a future version of Aaron? I just don't understand how seeing Aaron would startle Flocke the way it did. It seems to be a boy from MIB's past, either Jacob or somebody else MIB used to know.
MIB looked at the boy as if he were a ghost, not as if he were a flesh-and-blood, time-traveling, person... MIB is seeing visions just like everyone else on the island has seeen visions of the things that haunt them from their past.