What if these mysterious Warden allies are the Red Templars?
Also, it has to be asked, do we know that all those plot flags fire properly in terms of dead architect or not? I never get Nate's quest because it thinks he died in my actually-fully-upgraded-so-no-one-dies Keep.
Same here. I got Awakening epilogues where Nathaniel brought new respect for his family name, and his sister's kid got some lands (no idea why they went to Kirkwall then, maybe they were visiting Nate's foster father?), but then I checked the flags via console, and everyone was dead, including Anders, lol. I fixed them, but the quest glitched anyway, I had to teleport there to see Nate
Or, perhaps they don't need to masquerade at all. Maybe the Wardens just think they're collaborating with some not-really-evil, totally-not-insane templars at first? That would be consistent with Nate's "It's ... complicated. Let's just say we live in strange times." comment.
edit: Actually, the more I think about it... this could be something! The templars approach the Wardens about something of cool and scholarly value in the Deep Roads, since Wardens are Deep Roads experts...? Hey, we found all this red lyrium, let's all go look for it together! Yay, woo hoo, friends, pay no attention to those red crystals growing out of my skin... 
I don't think Nate was talking about RT, because they don't seem to be the Deep Roads experts. He was talking about somebody who knows the Deep Roads well. I thought about the Legion of the Dead, but he says they are not drwarves?
I think Nate met these guys (gif):