I say this with the utmost love in my heart: Only NERDS care about canon and continuity.
Cataloguing all the
Universal Streams including the one
micro-continuity from that one Black Friday pack of toy can be a hoot and I'm here for the nerderry of it, but at the end of the day it's all made up anyway and the average consumer isn't gonna care what is in what continuity. Is Roger Moore Bond the same guy as Sean Connery Bond? It doesn't matter and nobody cares and people still went to see the films.
When it comes to franchises with multiple continuity, it's best to not lose sleep over it. Continuity is your tool, not your master.