Why do I feel like Touma's father and his assistant are in some kind of Relationship...

OMG. That's what I thought too. And because of that he's jealous of Touma.
So they are together or he at least has a thing for him is what I thought.

Or another possibillity that came to my mind was that he maybe hoped that he would succed the company, since the Boss had no children and was therefore shocked, that he adopted one.

Either way he's an asshole.