I am glad that you understood that section. If one understands that, one can eliminate Sakkaya Ditthi, as you seem to have.
1. You wrote: “How an extremely small bit of matter powered by kammic energy can create so much suffering.”
– Yes. Many people may not fully understand how small a suddhatthaka is. It is much smaller than an atom in modern science. Yet, the “seat of the mind,” hadaya vatthu, is just a single suddhatthaka energized by kammic energy. Our huge physical body is no different from a huge tree trunk (i.e., lifeless) when that gandhabba with the hadaya vatthu leaves (at Death or in an NDE/OBE).
2. You asked: “1. looking from POV of bhavanga, sottapana has removed all apayagami bhavanga. because all citta/cetasika corresponding to those strengths are removed/reduced in javana. right?”
– You mean “temporary bhavanga,” not the “bhavanga” one is born with. Yes. One can get into an “immoral temporary bhavanga” if a tempting arammana comes to mind IF one still has anusaya. So, since a Sotapanna has removed “apayagami anusaya,” their mind will not be tempted by such an arammana and thus will not get into such a “temporary bhavanga.”
2. So, we can revise your #2 as follows: “2. As we progress, the possibility to get into more such “temporary bhavanga” are removed because less and less arammana with which we get stuck via tanha.”
– Here is another way to say the same thing: “As we progress, the possibility of getting into bad gati will be removed because corresponding anusaya will be gone.”
4. You wrote: “And sense restrain will take care of food coming through contact, isn’t it?
We must deprive fire (of jati) by reducing/stopping the throwing of wood logs (through four foods) in it and also stop the supply of oxygen (three san), right?”
– That is exactly right.