If I'm reading the mail here correctly, on freighters the number of cargo carts/pallets is being determined as a proportion of the max cargo weight...e.g. 40% load gets you two of five carts, 60% gets you three, 80% four etc...
I think a better methodology would be to determine the number of carts based on an average pallet weight--6500 lbs/3000 kg is a good round number for the big pallets, and half that for the small half-width ones--and then cap the number of carts at 5 to observe the aforementioned sim limitations. Bringing out multiple trains (similar to the way multiple pax busses are dispatched for large pax loads) would be more realistic still.
An MD-11 or 777, even with a relatively modest load of 100,000 lbs of freight is going to need way more than the six carts (3x two cart trains) I'm seeing.
Alternatively, allowing the user to set a fixed number in the config would be a nice option.
edit: also, in freight operations, we almost always "cubed-out" before we "grossed-out" the cargo bay, meaning that we (usually) filled the available cargo bay volume long before maxxing out the gross weight. So weighting things towards sending five cart trains as a matter of course would be a better (more realistic) option than singles or doubles, especially with large freighters like the MD-11/777/747.