I would have to wonder if the shorter one was intended for KR's ?
There are good reasons why we run less oil in a race only engine. If for some reason the shorter part never got designated with an "R" part number the spare parts people might never have known they were meant for different application. This would be a purely technical error on HD's part I know. But those things do happen from time to time.
The only other explanation that comes to my mind is that originally the gearbox oil level was set higher. They did have problems with early gearboxes and maybe too much oil was found to be a factor. But if that is the case I would suspect the shorter one would have coincided with the 1-1/2 pint the FSM calls out for capacity.