Im inclined to agree with the Op on this, having extra science console slots for say the science ship is a pretty useless bonus if you dont have a science commander boff slot to take advantage to them.
Also...if you dont have the commander slot of your ship class(eng/sci/tac).....then your train bridge offiicer skills are useless...eg: Gravity well 3.
This matter also effects ships like the bortasqu and vestas, both of which have BO slots that dont reflect the class of ship its supposed to be.
Quick idea...........ships with 3 variants..........universal comm slot.....problem solved
All universal boffs and all universal console slots across the board.-problem solved.