Just an update (can't edit my post sorry).
The .cbz files I referred to in the OP were converted with KCC, to the exact Libra 2 resolution (1264x168)
I tried converting again, but this time to a bigger resolution but same ratio (1817x2415), and for whatever reason this has fixed the issue!
There's still some hiccups, where it'll crop one side of the page but not the other, but it is much more consistent than before. I'd say about 90% of pages crop properly now, whereas before it was about 50%.
The oddity still persists where if I choose semi-auto on a page where only one side has been cropped, it'll correctly show margins on both sides. But clicking apply has no effect.