Let's assume for a moment that the calls were real. What do they tell us?
Did coworker recognize JF's voice? If so, was that because he had a habit of calling? If he were a "pest" so to speak and called often and bothered his mother while she was working, perhaps her initial assumption might have been "there's no real problem."
From what's been reported, RVW (raspy voiced woman) asked JF if A was his mother. That would indicate that she didn't know the mother. JF supposedly said "Yes, ma'am."
Now, I know the south is different, but around here (Connecticut), 12 yr old boys don't generally call people ma'am. (perhaps the aunt could comment regarding whether that would have been normal for him?) Might that suggest that RVW was an older woman? Or maybe it means he didn't know her name?
And some further thoughts. If there is a roommate, is that a reference to the step dad? If not, is roommate male or female? If female, did she have a boyfriend? Who else had access to the apartment? Was the door kept locked? Did mom/step dad/person she was living with have a drug problem (which could have resulted in other unsavory types being in/around the house? Was JF left alone regularly, and if so, who knew about it? Why were mom and step dad living apart? (Given that she was living in the same complex, I do wonder if they had a tiff over something and she was staying with a friend for awhile.)
Assuming the phone calls are legit, I don't think the step dad would have had time to do anything with the boy. (That is further assuming that the police know his whereabouts over the time since the abduction, and that there are no large blocks of time where is is unaccounted for.)