No, it really doesn't depend on that. Shifting every ton once will always be quicker than shifting it twice. That's even before you consider carrier jump times.
You can always set your jumps for when you end your session so its at the destination for when you're ready to log back in. This thing is going on for 4 weeks so will always be plenty of time to jump your carrier when you're taking a break, unless you're the sort of person who can fill/empty a carrier in a single sitting!
We can play with some numbers.
Let's assume no long SC distances at either end. A hyperspace jump and alignment ready for next jump takes about 1 minute on average. Let's assume you can park the FC around the same planet the source station is and the time from FC launch to station and docked is... 2 mins? Assume same 2 mins for the return, especially since unloading to FC can take quite a few seconds with no way to make it faster (loading is quicker). For the non-FC version, we can assume a 2 minute SCO run to the station and docking. 1 minute to undock and align to jump. At the delivery end, we most likely have at least 1, if not 2 jumps to Minerva from wherever we are parked. Let's be generous and assume we get a slot 1 jump away.
So, FC version per run: 2 mins (FC to station to buy) + 2 mins (station to FC to store) + 0 mins (offline jump - not every time, just including to make a note) + 1 min (undock and align for jump) + 1 min (jump) + 2 mins (FC to station to deliver) + 1 min (undock and align) + 1 min (jump) + 2 mins (return to FC for next run).
Non FC version (variable jumps): 1 min (undock and align) + 1 min x N (N = number of jumps to target system) + 2 mins (in target system to SCO and dock and buy) + 1 min (undock and align) + 1 min x N (number of jumps) + 2 mins (to make it to delivery station and dock).
FC total time to get at least 1 unit transferred is 12 mins.
Direct (not using FC) is 6 mins + 2 mins per jump (1 min extra each way).
This roughly means that if you need to make 3 jumps or less, you might as well not use the FC. Above 3 jumps then the FC method becomes more efficient.
Play with the numbers how you like if you don't like the numbers i'm assuming, there will still be a point at which the FC becomes more efficient.
The question is, will there ever be a point where you can't get a full cargo hold in every run at a system within 3 jumps?