Lots of lengthy continuums of stories or big fictional worlds have taken things out of continuity or refit them. It just doesn't matter much, to most fans, most of the time. It probably, here, doesn't even matter to most Star Wars fans.
I have to imagine the average Star Wars fan doesn't even know what EU stands for in relation to Star Wars.
There's a nice piece of filler/intro art in one of the Who comics laying out the various incarnations of the Doctor, how they fit together, and Peter Cushing's Dr. Who, without attempting any in-story connection.