I just got off the phone with an agent from cic, and he said the same thing as you. He was firm with saying that my dad should NOT be included as a dependant. And my mom’s marital status have to be legally separated because in the context of ircc guide, "legally separated" means married but are no longer living together. And the answer should be based on the real, ongoing relationship right now, not just because there’s a marriage contract binding. There is no relationship between them anymore therefore she is legally separated and my dad will not be included in the family size. Although he’s still in Additional Fam Info. And yes, the agent said a letter of explanation will suffice. But I will also have my mom get Affidavit to support the explanation, just to be safe.
It all makes sense now. Finally I can breath after being up all night stressing about it. I’m really grateful for all the response here. Thank you sooo much!!