You are not factoring in the steel cross members that have been removed for the moon roof. And why would there be any difference between models? I'm not an engineer but you are not making any valid points.
Crossmembers can be done differently, instead of a bunch of little Crossmembers, you can do a smaller number of larger ones. There's a photo somewhere comparing the Crossmembers on the moonroof vs non moonroof explorers. While yes, the non moonroof cars have a few more smaller Crossmembers where the moonroof would be, but the moonroof models have a large boxed in area around the moonroof with larger Crossmembers. Think of a load beam if you remove a weight bearing wall in your house, you just require a substantially larger beam to support it over the opening vs a larger number of 2x4s.
Keep in mind, Ford has the same roof strength for a moonroof vs non moonroof model. That means their engineers designed and calculated them to have the same roof strength, and the roof can support the whole weight of the car in a rollover. If the roof can support the car, barring some sort of fastener issue (ex, the rails screw into factory installed nutserts that have a pullout force limit), the roof should hold whatever weight you need.
FWIW, I am an engineer. You might not be getting the validity of my points, and that's fine. That said, I think there's still some element of fear about explorers at Ford from the whole rollover thing in the 90s. I wouldn't be surprised if they went intentionally cautiousnfor anything rollover related as a result. Hell, as of a few years ago, uhaul wouldn't even rent trailers to explorers.