1.There's a whole lot of assumptions going on there and the prior post.
MC's mom was quite...weird and there's a lot going on there but I'm still going to hold off on the idea that she's a monster of any kind.
If she was there is no way they'd allow MC to go be they HERO or SIN, he'd be an oddity and would need to be studied no matter how many strings MC's dad tried to pull he'd lose his child for certain.
All I recall of the hospital/clinic MC goes to is that I recall MC mentioning it was a private one or something along those lines so for all we know it has zero affiliation with SIN or HERO.
Deny it all you want but there is almost no chance mum is fully human, not after the hiding from thunder scene
2.
I've no idea why they would let him go, the only assumption i have is that mother was mutelated or eaten and so they never had the opportunity to test her and find out she was a monster. Mc not being physically any different from a human is a stretch, but perhaps some of the monsters that give birth can decide whether the child will be biologically of the father's species or mothers.
3.
Considering dad's connection to Dexter and it being the same hospital that he was brought to after his mother's "weird" death and after becoming a superhuman and passing out, it only makes sense they are connected to the world of supernatural. Also, it's the only possible time MC could have met Ella in his childhood, it would also make sense why he doesn't recognise her, he probably brainwashed at the facility.