I just designed custom gearboxes for a WCD we are hopefully going to build. Based on the 221 "Super Light Toughbox Transmission". BTW thank you Anthony for posting CAD on all your stuff.
The reason being I needed something that would easily be able to be bolted on frame rails and it turned out it was was easier to just CNC out two side plates, then try to come up with some kinda of mounting system for the COTS ToughBox. It also is cheaper for us cause we already have the gears and shafts.
For me and our team, if I can I would use a COTS gearbox, but when trying to integrate a COTS gearbox takes up more time/work then just doing a custom gearbox, I will just design something custom that fits nicely.