So that toggle appears to have fixed the problem for certain movies, but not all. I'm running into a couple different issues here across several of my iso files, and it's driving me a little crazy lol.
The files all play perfectly fine when mounted. However, when I go to convert the iso to an MKV, I run into one of two problems. I either get a failure in CloneBD similar to the disc/log I attached in my original post, or I get a failure in MakeMKV. These problems can either manifest individually (errors in one but not the other) or in both applications. Discs erroring in one application that convert successfully in the other all appear to play successfully.
However, even when they successfully convert, I run another problem. Roughly 1 in 5 movies convert without an audio track, at all. As far as I can tell, this only seems to be affecting movies that error in CloneBD, but work in MakeMKV. Batman v Superman is one of them, 10 Cloverfield lane is another. Super confused by this, considering they all play perfectly when mounted as an iso.