Does the load when X available order actually work? I remember trying to use it to transfer infrastructure, and if there wasn't enough it would put a message saying it failed to load fully, but would proceed to the next order anyway.
It works for me, in my save mercury is basically always on 0-7k stockpiles on every mineral and I have multiple fleets with different destinations that will go there and wait if there isnt enough of a particular resource.
I will generally set both a maximum pickup amount and the minimum available amount when setting up their orders. So if I want 4k of every mineral I do "pick up max 4000 when there is 4000 available". If the mining planet has a population I usually want a reserve and Ill do something like "pick up max 4000 when there is 24000 available", in the last instance I essentially reserve 20k of that mineral - this is important to do because I believe that "load when X available" does not necessarily adhere to reserve levels set on the colony minerals screen.