I don't think there's a hard and fast rule for what is and what isn't canon. From my experience on the boards, it seems the generally accepted rule is that alternate realities and other universes where there are alternate versions of characters are not canon. However, for multiversal beings such as LT and Phoenix, ALL appearances are canon...even What Ifs.
I don't really agree with that, because What If's are really hacked plots sometimes with ridiculously high and low feats for even abstracts - like the time LT was unable to defeat Korvac and had to seal off the entire universe to put him away. And there are several What If's featuring really low showings for Phoenix...although it's easy enough to blame it on the host, rather than a problem with the Force itself.
Either way, that seems to be the generally accepted way of handling alternate realities and such. take it for what it's worth...