Even though N released his dragon we don't know the fate of Hilda/Hilbert's Reshiram/Zekrom. Maybe Mewtwo's the same way. Let's say Red never caught it or let it go and Ethan/Lyra ended up catching it in HG/SS. But we will never know for sure unless any of those characters show up later on down the line and tell us in their own words what happened to it.
So right now it's pretty much Schrodinger's clone cat. Was it caught in canon? Was it not caught in canon? Is this some other Mewtwo if it was caught in canon? So until proven otherwise (in somewhere that isn't the anime) Newmew is fully open to interpretation.