I think that there's one Knight-Commander per region, and I base this solely off of Gregoir being a Knight-Captain. I feel like there was some impression given that the Knight-Commander of Ferelden was in Denerim, but it was never explicitly stated. (And yes, I could very well be doing mental gymnastics trying to make the lore fit with the game, when Gregoir really should have been a Knight-Commander all along.)
Wasn't he called Knight-Commander though? That's what I remember, anyway.
Edit: whoops,

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He tells Hawke to her face in Act 1, "I've been hearing strange rumors about you/your sisters, Hawke. I hope they're not true." He knew Hawke/Bethany were mages from the start, the whole "Cullen is oblivious" thing comes from them failing to put a dialogue check on the "mages are not people like you and me" line to exclude mage Hawkes. It was a game mechanic error, that they've brushed off by joking that Cullen was an incompetent Templar. But that first line is right there in the game, that can't be taken back. His motivations for not pursuing are anyone's headcanon, but he certainly knew about the Hawkes from the start.
Ah. It's been a while since I played the game, I don't remember the exact dialogues. However, confronting them with "strange rumors" isn't quite equal to knowing with absolute certainty that they're mages. There's still some room for doubt, especially if one wants to doubt.
I seem to remember the whole thing being more widespread, but if it's really just that one dialogue, it could just be that he simply forgot himself for a moment and went into impassioned speechifying mode without realizing who he was talking to. On the other hand, there has to be a reason why he doesn't just bust them on the spot for being apostates.