For example deflect instead of binding to lectins in your system, to clean you out, could bind to less offensive things in food.
The others could be for maximum absorption, or other conflict that may limit their uptake.
Some thing can counter act each other, like quercertin and Trehalose. They perhaps neutralize each other.
Probiotics I would be curious if they manifest in the stomach or small intestines at larger amounts, so when you do eat food you are effectively moving more through you, but I don't know. After all different foods can cause a decline in the entric bacteria so why not have as many as possible to keep the balance on the good side.
What you said about the Deflect makes good sense to me, and the part of competition for absorption may apply to amino acids.
I would expect that most probiotic bacteria that entered the low pH environment of the stomach would be killed if they are active. Stomach acidity is actually lowest just after a meal, so that might make for a better environment, but that shouldn't matter if the bacteria are in spore form. It's my understanding that they colonize in the intestines not in the stomach. On one hand, taking with food gives them something to eat immediately. On the other, the bulk of the food could sweep them out before they have a chance to attach. I don't know which is the case.
I find it difficult to take anything on an empty stomach, because as soon it's empty the clock starts on me getting quesy from hunger. Taking away from food requires taking on an empty stomach and then waiting a while longer before eating.