If I’m going to second-guess the experts, I have to use my own intuitions based on their data, methods, intermediates, and conclusions. I’ll admit it isn’t “pound on the table” proven, but when, for instance, MOD500 is replaced with something more detailed, the whole thing can be re-run. If they did it right, it probably wouldn’t take more than a day or two.
You know more about this than I do, why don’t you go right to the paper and see what (if anything) they’ve done about the issues you see? That’s part of why they made it available now, rather than at publication.