My theory on this is that:
Mwu did survive the explosion except was left drifting in space on the verge of death and was picked up by the EA in the area. Due to his critical condition he had to be kept in stasis to heal for almost an entire year and while in stasis had his memories edited with a newly developed system that is the one they now currently use on Stellar, Auel, and Sting. When he came to they made him a Lieutenant (i think that was his rank), told him his name was Neo Lornoke, and gave him Stellar and co. In regards to Rey I believe that he was a clone that Rau had made of himself (in ref. to reason #7) in the case that he should fail in causing havok that he entrusted to Chairman Dullindal to raise secretly and only told Dullindal that he had would have piloting skills at or exceeding his level. He of course did not tell Dullindal of his secret intentions to cause the annihilation of the human race.
And that is my theory on the Neo is Mwu and Rey's Secret paradoxes.