Luke's conversations with him are stated to be non-canon...so I assume this is a gameplay mechanic, and all the endings are merely prerequisites for the player to get the "true ending" (which doesn't exist yet).
Time travel has never explicitly been related to the main plot (other than shattering I suppose, if that counts) so I wouldn't assume this game has the same meta aspects of Password. But, I could be proven wrong with all the content still to go...