Yes, I went there again. After spending too much time collecting Monster Hunt boss decklists I just couldn't stay out of Rumble Run either even though there's lot less incentive to play the mode after your first win. Hopefully someone will find joy from this thread anyway.
How I think the decklists work: each Shrine has 30/31 card decklist and all encounters with smaller deck sizes are somewhat randomized portions of those decklists. And yes I'm quite sure some of the decks do have 31 cards and it's just not me seeing extra cards but I haven't figured out why it's so.
I've been trying to build their new decklists from scratch, just using data since the 10th. I can confirm you aren't crazy, there really are decks that have 31 cards in them. Observations so far seems to indicate that the shrines with 31 cards decks are still fixed, for example, you cant have a deck with 30 cards at round 6 but it becomes 31 cards at round 8. I have a suspicion that Jan'alai's Mantle and Shirvallah's Vengeance are also 31 cards, but havent been able to confirm yet.
Also damn, getting those decklists is hard work, especially for the earlier shrines.