This isn't me saying that I think the rating reasonable or that I agree with their decision to keep it at EF4 180 - but I do understand where they are coming from if their concern lies with such simulations containing too many generous assumptions, which is likely to me.
If that is the case, then the fact that they weren't getting values well exceeding 200 mph means that if there is something wrong with the assumptions they made (and there very likely is, when considering the real world vs. idealized simulations), these numbers cannot be 100% trusted, even with Monte Carlo simulations. They add good credence to the fact that it likely reached EF5 intensity, but it's not as set-in-stone as structural damage calculations would be. Unlike with structural damage indicators, there isn't a standardized way to approach granting a rating based on the simulations. I was hoping Enderlin would get the ball rolling when it comes to this type of thing, but it appears that it has not (at least, not yet).
Also, it is worth mentioning that the numbers they are using are almost explicitly median/mean values and ranges. They almost certainly did get runs below the 200 mph threshold for any one or more of these DIs they tested on, and if the amount of runs pointing to EF4 rather than EF5 intensity is within a single standard deviation, the decision to keep it at EF4 is honestly a good one to me. FWIW, I do still think it reached EF5 intensity, and it should be rated as such. Of course, I'm throwing out a lot of hypotheticals here, and I could be wrong on what the true reasoning is... but their decision to state outright "the tornado very highly likely reached EF5 intensity" and not say "certainly" does some heavy lifting here.