Please excuse me, but did FD officially announce that you can put Ships loaded with cargo into the shipyard ? Because as of now, that is not possible, hence the question of the OP would be a clear "NO - that is not possible".
Regarding costs of the ship transfer:
We don't "know" anything yet, but when we take the numbers provided in the streams and screenshots (which may change, or not), you can do a rough math of costs:
For a Beluga (a trading Cutter would not be that much 'cheaper' i a assume), 40LY would cost 579,850 CR. That's 14496.25CR per LY. If you want to get that "quick" to Jaques as an example, that would be 22.000LY x 14496,25 = 318.917.500 CR - not so reasonable.
If you would like to do Sothis/Ceos Runs, and assume a total distance of 450LY to travel (and 'summon'), than this would be still 6.5Mil CR for that trip.
I really don't see the point of the discussion. It is not "button to win" or else. It just gives player a convinient way to get ships to a location, if they really want it. Moderate costs in the bubble, really really high costs, the further you go out.
If you are in your "big" ship, and just want to get your Explo-Vessel, or Fighter somewhere inside the bubble (or not to far out), it does make sense, every other scenario, i don't see this work for a reasonable amount of Credits.
just my 2CR,
o7
Of course, just made of assumptions right now.