It's a hard call at this point. Yes, Thomas learned some elementary or rudimentary spells, but on the surface anyway, he didn't seem interested on learning more. Was that because as a vampire he didn't think he needed to know more? Did he fear his father would kill him outright if he did? Remember Thomas was very into playing the dumb playboy type to stay alive, when we first meet him because of his father. Or is this in fact as far as Thomas can go with his talent? He has had his chances to learn more, he lived with Harry for a year and he was a protector of the Paranet and had contact with Elaine. Was he also afraid of the Wardens if they figured out how talented he really was? One problem with that if I remember correctly, Harry seems to have a "spidy sense" vibs when he is around someone with considerable magical talent, he has never mentioned it as far as Thomas goes.. But then again I could be remembering that wrong, and Harry also has been clueless at times. One more question, and it may be elementary because Thomas was very young when Margaret left him for Malcolm.. Surely she would have known that as her son, Thomas potentially had talent, maybe lots of talent. She had to also know how dangerous a WCV wizard would or could be. So knowing this, why did she leave him behind? Yeah, maybe roll of the dice, no talent, little talent, potential kick ass wizard, worth the chance? Or did she have ways of blocking that aspect of her genes when she conceived Thomas with Raith? Or did she have another way of knowing her six year old son's magical talent would be limited at best?
You are absolutely correct that Thomas has had the opportunity to learn more if he wanted to. It brings up the question of where he learned his basic spells from. Did Harry teach him that? If so, why did Thomas not learn more? It very well could be out of fear as Mira suggested. Fear of the Council or fear of his father/Lara viewing him as a threat.
As far as Harry having a "spidey sense" with regards to magical talent, he can tell either through direct physical contact with someone or by deliberately reaching out with his senses to scan their aura. Harry has said that when he touches another person with magical talent it feels like an electric shock with bigger jolts corresponding to bigger talents. If I recall correctly, actively sensing someone's aura is harder to do and more invasive. It is uncomfortable for the wizard having their aura scanned and therefore not considered polite. Most wizards do not do that for that reason. In addition, wizards can shield their aura at least partly. As far as Maggie Sr goes, we know that magic is passed along the female line. Therefore, she would have had to know that Thomas would have had a chance at inheriting magic. Magical talent does not express until early teenage years and I do not think there is a way to gauge magic talent before it is expressed.
I have wondered a lot about what made Margaret decide to leave Thomas behind? In some thoughts she is the villain, in some the victim. Maybe she thought that a life on the run would be less safe for her child than staying at home with his abusive father but being integrated into a strong family clan with at least one loving sister (Lara).
Or was she forced to leave alone in a situation of flight or death?
I think somewhere there is a WOJ that Maggie had already met Malcom and was pregnant with Harry when she left Raith for good and went into hiding. If I was guessing, I think she left to protect Harry and could not safely take Thomas with her. Especially if she knew Harry would be starborn and was trying to keep Raith from getting his hands on Harry.
Or did she make a bargain with someone/fae (Leanansidhe?) or with Lara for protection for Thomas?
I do not know if she made a bargain with Lara, but the author states that she did not make a bargain with Lea covering Thomas because she figured Thomas was a baby shark and could protect himself.
Did she suppress his magical talent to make him seem like no threat to Raith's power?
Until he was old enough to express his magical talent there was nothing for her to suppress. Unless she was able to put some type of shield over him tied to his lifeline/soul before he expressed his talent in order to hide it from prying eyes. We know she tied the death curse on Lord Raith to her kids life, so it is possible to tie a spell to someone.
How involved was she in the plan to produce a starborn child? And when her first attempt failed, she left her failure (Thomas) like garbage to try again?
Someone asked the author this specifically. He said that Thomas was not planned and was just the result of having lots of awesome vampire sex. No word on if Harry was intentionally conceived to be starborn or not. We know that Maggie Sr loved Harry's father so he could just be a result that love and cosmic coincidence or she could have been shooting for a specific time to become pregnant by Malcom.
There seemed to be some love between her and Thomas, or she wouldn't have linked her sons' amulets to trigger her appearance during their soul gaze. But for her to do that, she must have known that there will be a future second child.
Was she prescient? Or did someone tell her? Or did she plan it all ahead?
She knew she was pregnant when she set up the amulet linkage. She might have even had Harry at that point. In the amulet message to Thomas she told him to look out for his brother. Thomas had memories of his mother and already knew that he had a brother.