Yeah, but that is probably due to the nature of the rules. As far as the system goes, all the other vehicles work the same too.
That was what I was suggesting with the Shipboard Systems (Shuttle) idea. Basically, I can see some overlap. For instance a pilot who is skilled in 23rd-24th centruy atomposheric creat is probably cable of piloting a shuttle, much the way a 21st centruy prop plane pilot has some overlap with the skills of a jet pilot.
But that has some rough spots too. THw workbee is operating basically the same as a shuttle. If you tack on a impulse or warp module, or one of the super/killer/assault "sleds" then you would need another skill to cover it.
Personally, I think Shipboard Systems should work for all vehicles with a LCARS type interface (or similar for pre-LCARS ships) and vehicle ops reserved for craft with steering wheels, flight sticks and such. I'd probably let one substitute for the other at half ability it it was related.
For instacne, FLight Ops can probably overlap a beit with most flying vehicle ops, and Sensors are probably sensors.