I don't fit scoops on any of my ships except for my "taxi" and exploration ships and have adapted to the idea that I always travel in the taxi and then transfer in the ship I actually will need. The cost isn't really a big deal but the time involved took some getting used to.Good point. FDL is not meant to travel. I have to consider some transfer time and fees
My approach has been to plan ahead and try to do the taxi-travel and ship transfer just before logging out so that the ship is where I want it next time I log in. Failing that, I will travel, set up the transfer, and if it is longer than 15 minutes or so travel to some other ship location and do other stuff there until the transfer finishes. I have two mining ships parked at good mining locations, for example, that I can go to and do some mining while waiting. My taxi has a jump range of 70 Ly so I can really get around nice and quickly to accommodate this approach.