Ok then. Let's look at another point. Your decision to clear the Consort's name of the framing charges in
Mass Effect 1 does not properly transfer to
Mass Effect 2 (one of several decisions that is glitched in the transfer). Does this mean that it is "canon" that, no matter which choice you made, Shepherd never helped Shai'ira?
Because otherwise you have to realize that technical issues can adjust the story, without actually affecting canon. That an inability to transfer save files and take your decisions into account does not invalidate those decisions. We already know that system limitations are responsible for things like
P3P not getting
The Answer, and not being able to load your save file from
P3 or
FES into
P3P, so what else might have been decided as impossible or impractical because of technical restrictions?
The story you play is the canon. ATLUS moves the story forward in the best way they could. They had to make a decision one way or the other, but that doesn't mean that they are disallowing the choices of fans of the other side.