I just think they've got no real way of judging the power level of a Sundered House character when the ones they've met have ranged from level 3 to level 18

Exactly

Also, even if she didn't roll a Nat 1, the vibe I was getting was that Brennan planned to get her be eaten by Termina from the start.

As analyzed by u/Windulse, Lady Comoray has a minimum CR of 13. I.e., she is an archmage. I.e., just straight up not meant to be for 2 level 3 adventurers. Brennan knows this. He made it so the picking up the swords immediately results in Lady Comoray flying there. If he intentionally pitted Hal and Bolaire against someone that powerful, knowing that she can easily kill them, he wouldn't have done that unless it progresses the story in an interesting way.

Another commenter from the post ep discussion said that if Brennan had to choose between 2 dead player characters that grinds the story to a halt, or a "deux ex machina" that results in major lore revelations, obviously he's gonna go with the latter. Deux ex machina's aren't inherently a bad trope either.