It largely depends on the nature of Corypheus' return. We know that he disguised himself as still being Larius/Janeka for his research purposes into Red Lyrium. Perhaps he convinced people to ally with him by first appearing as such, and then morphing into his true form to show them who he really was.
I'm not saying Cory would've blabbed his thoughts to all of his people, or even Alexius really (because if you go Templar route Alexius is killed because he outlived his usefulness, indicating he either wasn't high up in the Venatori ranks or Cory took the Felix thing into consideration) but I am saying that given what goes on in the story Alexius' keeping Felix out of the Wardens makes sense. For all we know Alexius found out on his own (this is a Darkspawn Magister after all, which merits investigation).
Especially in the bad future, when Wardens would've been corrupted and he'd find out, and thus def. kept Felix out (if he was still alive at that point).
Regardless, even without the specific Warden stuff of the story, the whole "losing your status as heir" thing would be a reason he might've kept Felix out. Pride and all that. Felix is obviously a strong person, given that he hoofs it all the way back to Tevinter and gives a stirring speech to the Magisterium, never mind how long he's been Blight-sick and still seemingly healthy when it doesn't act up.
As for Calpernia, that's something I need to think on, as Cory has both Calpernia and Samson at his side in my 'verse.
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