I'll just preface by saying this is a lot, an awful lot of speculation. So, here goes nothing:
We know that step-dad was strict, used some really old ways of disciplining his step-son. The mom appears to have never interfered with any of it, or disagreed at any point.
With her reporting the noise coming from his room AFTER she asked him to go to bed, we can now think that if she condoned the step-father's punishments, she went after Sebastian to punish him for not being asleep (if the step-dad really wasn't at the home)? This could've left him in a bad place mentally, making him leave on his own, or this could be the moment where something goes wrong and he's injured. Much like other stories we've heard. MOO.
Or maybe she went to check on him, and he already wasn't there, but because she was in a call with the step-dad they decided to report it in the morning? IMO.
I don't think we can completely rule out the possibility that he was tired of their "hard strict discipline" and just ran.
Edit to change some punctuation.