*facepalm*
The whole Tau Sigma issue is not canon because it's fanmade but the Capellan refugees issue is a canon one, easily deduced. It's likely to be one of the major issues of the early Post-Capella period.
Same for the Sol Gate. The GTI Melia is not canon, nor is Inferno, but the fact that the GTVA has the knowledge to reopen the jump node after the Second Shivan Incursion is canon. It's even mentioned by Petrach at the end. Reopening the node would be an important Post-Capella issue, possibly much more important than the Capellan refugees.
I'd like to know if you can deny those facts. 
Sure, sure, we can suppose that these logical issues will be handled logically. But that doesn't mean we 'can't deny' that this will happen. We can deny it and instead suppose that in FS3 the GTVA would've become a whimpering, huddling wreck.
And if FS3 did that, instead of dealing with the refugee issue or the return to Earth, that would be canon. So yes, until it's canon, we can deny it all we want.
Shockingly, I completely agree with Mobius on this point. One obviously can't say that any specific campaign, or even idea, taking place after the end of FS2 is canon, but the two issues he mentioned are established by the canon material of FS2 and would obviously be concerns in the period afterwards. We know there are now 250 million Capellan refugees that the GTVA will have to deal with somehow, and we can at least surmise that further research into studies of the Knossos gate will eventually lead the GTVA to a point where they're able to construct one of their own, or at least leave them far closer to being able to re-establish contact with Sol than they were before FS2. None of this is coming from outside of the game.
See above -- it's very logical, I agree that this is what would happen next, it's all firmly based on canon, but we don't know it would happen until it happens, which it never will.