Responses
I feel like the many questions you asked is answered in the story XD
MC is a beta not a dormant Omega, he was turned into an Omega by the ML. MC stabbed him because he was scared for experiencing alpha pheromones for the first time but he didnt mean to stab ML. ML's dad adopted him thinking he was a beta but when he found out he's am Omega he told him to stay away from his alpha Son.
Its very obvious ML's dad is very traditional and can be controlling. He even arranged a marriage for his son probably with someone that have influence

um... good story i guess? liked the concept but it def could have been fleshed out more. i.e how did he know that mc was a dormant omega? was mc stabbing ml the reason that the dad made him go to the annex? what kind of dad is the dad?
still, a good read if you want some pwp