No, that's not the problem I have. In fact I don't really have a problem with that (other than supercruise which ship transfer doesn't touch), I have a problem sitting in a star port in my Corvette knowing if I had my Python I could take that juicy outpost cargo hauling mission, ship transfer fixes that, and it happens A LOT.
Well, for that reason I make a conscious choice which ship to fly, and the Python is my most often flown ship; I could afford an A-grade Anaconda, but I don't, I take the Python for the flexibility to use outposts and accept that it is weaker, hauls less cargo and jumps not nearly as far. That choice and its drawbacks get basically neutralized if ships can be transferred instantly anywhere with a shipyard and I would be technically better off just having both ships and switch instantly on a whim.
But alas, we are turning in circles, while FD stand firm on the matter. So to repeat: I implore you, Michael, keeper of the lore, to not include any official explanation, make the lore pretend ship transfer takes proper time and some hired pilot to perform it. Don't treat instant transfer as anything but a convenience game mechanic, just like instant repair and instant refuel.