Baka-fool : Mandy is a fox calculating many aspects of everything. That's no new info.
Here, if her "super-soldiers" happen to be her offsprings, she'll have much greater control over them, since they will still obey their mother who raised them.
I think that's probably the most tricky part of her life-long plan : she's instilling love to her children to ensure control over them, while she clearly does not love them herself.
As for the fathers' identities, here's what i thought of :
-> Both Jr and Mini are Nergal Jr's offsprings, most likely they are twins. This was done with Grim's authorisation, since he wanted a child. He killed one of the twins to turn him bony, hence started Grim Jr's life.
-> The one Johnny is referring to in the conversation is the one they "created" during the night. I doubt Grim is aware of that one, and even if he is i don't know if he actually cares. Johnny thinks of the potential of his future offspring by comparing it with Jr's potential.