m sleem,
I know at first glance it appears that feeders over 600 Volts are susceptible to damage from overload since you can have a protective device set as high as 600%. But it's there for a reason... protective device coordination.
The MV cables are sized per NEC 230, such that the amount of connected load drives the size of the feeders. Everything can come on at full load, and the feeder must be sized to accommodate that load.
The protective devices are allowed to be so large relative to feeder capacity per 240.100 because they are there to protect against short circuits, and by allowing them to be 3-6X, it gives room for the downstream devices to operate first. Note that 240.100(C) forces you to make sure the conductor can't be damaged during a short-circuit condition.
If you sum up all of the transformers or loads that are connected to your 13.8 kV 350 kCM cable, you should find that the full-load amperage is within the capacity of the cable.
I understand how it appears flawed, but it does make sense when you look at the big picture.
John M