I think #1 and #2 could be somewhat innocently explained by SM being a lazy parental figure with questionable judgment who didn't want to bother doing anything that wasn't the easiest thing with this kid. The Cousin It interview revealed a few things about her parenting in that household to me: she thought of Gannon as a burden at least some of the time ("I've been taking care of him for so long"), and she is the kind of mother who not only failed to prioritize keeping her own minor child far away from a police investigation, she tried to use her to establish her own innocence. So maybe if Gannon wasn't really all that sick, she wasn't going to bother to rally him for school or set a boundary later by saying he couldn't go to a friend's house (hypothetically, if he was even still there at that point).
However, I strongly agree with you about #3.
As I always say, evidence can’t be viewed in a vacuum. Lots of evidence when viewed independently from what’s beside it can be fairly meaningless. But it all has to be viewed as part of a whole picture.
So her letting him play (on the day he disappeared) after staying home sick, AND;
Letting him go off to a friend’s house without even getting a name, AND;
Lying about when he last left the house, AND;
Giving a ridiculous interview as she did, which was all about her, past-tense language, wouldn’t look at the camera when talking to Gannon, wouldn’t be on film at all, coaching her daughter, etc., AND;
Asking for a lawyer soon after her step son that she ostensibly loves, instead of putting up with anything LE throws at her with no worry about her own rights, as pretty much all concerned and innocent parents do, AND;
She’s the one who is seen last taking the child out of the house but returns without him.
You know what I mean? All together the picture becomes clearer and clearer for me even if some of the evidence only gets off a tiny bit of grime.