Ah those missions? With the mission specific caches into which you dump the cargo you sourced from somewhere, or from which you pick up cargo to deliver to somewhere? Yeah now that I think of it this should have been quite a no-brainer.
I've done a few of those, I think it was to build up some Federal rank.
That flow with the mission specific cache is not super obvious, but I can see how it would get complicated otherwise. If the commodities were transferred using the regular trading screen, the game could keep track of how much of the mission critical commodity you have brought to the mission giving station. That would be straightforward except that you wouldn't be selling the mission cargo and therefore receiving payment for it -- what if you sold more than the x amount required by the mission? Should it pay you 0 for the mission amount (as I don't think you get market price at delivery of the commodity in "source" missions, compensation is baked into the mission reward) and market price for any exceeding sales?
I think the current system is actually easier to understand: "Prepare to pay [avg] credits for X amount of Y, drop them here, you'll get paid for the mission (not the cargo per se) once it's all done."
Similarly I can see how delivery missions could get complicated if you just bought the commodities from the mission station. Firstly, the cost should be 0 because you're not really buying anything, you're just picking stuff up for delivery. And with delivery missions I think it's a case of "deliver this specific cargo", would it still be a success if you picked up nothing and just bought the cargo somewhere along the way or even at the destination market? Would it still count?
I would say the source and delivery missions are on par with the rest of the ED experience: Once you have done your research off-game for that specific type of mission, it's pretty straight forward. But like with most things in the ED UX, figuring out any process for the first time is usually the most challenging part, sometimes nearly impossible without 3rd party tools.