The dialog for transferring the cargo could have a minimum of 1000 cu or something (base the minimum on cu and not quantity), dock worker's union rules :)

Perhaps in station cargo transfers should require a fee based on mass and the cu per item, 200cu items being more costly to transfer that 200 units of a 1cu item, given the same mass.

@csgno1: perhaps in place of a minimum cargo, have a minimum fee.

Ever since the Trident was released, I have been a fan of allowing station-mediated transfer of bulk goods, while requiring manual in-space transfers for smaller amounts. So +1 to that.