You used to be able to retrofit multiple designs of the same size at once in SE3. Let's hope Aaron isn't lazy with the SE5 retrofit sub-routines!
Actually, I think the real reason why you can only retrofit ships of one design at a time is the max retrofit cost limit in SE4. This did not exist in SE3, where any ship could be retrofitted to any other design (of the same ship size, of course). Doing so didn't save any time, because all components started out "damaged" and had to be repaired.