Okay this is a complicated question to answer, also please answer to my chemical question on the other thread you opened too please.
If you directly pipe the Fluid into the Table, it will refill the Buckets.
If you have a Drum next to the Table, it will try to replenish Container Items with its Fluid too, directly while crafting, even with shiftclicks.
I just looked at the code and did find an Error there, so that might be the source of Water vanishing while the bucket is consumed without a trace, which is clearly a Bug that is gonna be fixed with the next test build.