I added a image of what might the beginning of a bus look like on gleba with the new mechanics in a image on the mod page.
As long as you have a simple less than check from the inserter into the machines where you make lets say nutrients from yumako mash you might have ~1 or ~2 yumako mash left over inside the machine but its very easy to deal with the tiny amount of spoilage that comes out before it gets sent onto a bus or train.
The furnaces are really easy to handle you just have a basic simple less than check on the inserter before it gets rehydrated then put into the furnace, then in the furnace it will have a big enough buffer to where it wont over fill and the rehydration stops until it goes below the threshold, same goes for the farms where you dehydrate the items right away.