It seems to me that KC/SI/AIT explicitly presents the choice of UTM as an unsolved problem, while coding theory and MML implicitly assume that you use your current coding; and that that is the part that gets people into trouble when comparing Zeus and Maxwell. Is that it?

I think more or less yes, if I understand it. And more seriously, AIT is in some ways meant not to be practical, the interesting results require setting things up so that technically the work is pushed to the "within a constant" part. Which is divorced from praxis. Practical MML intuitions don't carry over into such extreme domains. That said, the same core intuitions inspire them; there are just other intuitions that emerge depending on what context you're working in or mathematizing. But this is still conjecture, 'cuz I personally haven't actually used MML on any project, even if I'm read some results.