I take your point natalie_1982, it is perfectly understandable that DAWNU1 has no say in the seating arrangements, but her boryfriend certainly does!
As stonekicker advises, her boyfriend should advise his son that to place his partner elsewhere while his mother and her husband share the top table looks at best like some silent moralising point, and at worst like some kind of segregation - neither of which give any credence to her partner, his son, or the entire party.
I fully agree that wedings are a minefield of family issues, which raise their ugly heads. there is no way to avoid such conflicts at weddings, only to minimise them, and that is what should be done here.
I think that any outsider, with no knoweldge of the family, would see this as a slight to the partner of the bridegroom's father, and on that basis, it is unacceptable. If i were in that situation, I would discuss this with my sone, and advise him that my partner is now part of my life, and i expect her toe accepted and respected appropriately, and I am not prepared to be humilated by this unequal treatment of his mother nad her husband.
If my sone was taking issue with the fact that i was not married to my partner, I would remind him that the concept of respect and manners are facts of his life which I helped to teach him, and remind him again, that I would appreciate the courtesy of eqaul treatment.
Now I know that I - as we all are - am speaking from a detached point of view, and there may be far more to this situation than we know, but as it stands - a simple matter of ettiquette, this is neither the time or the place to make a point.
I hope you get it resolved DAWNU1 - you appear to be an innocent party caught up in familial machinations. let's hope good manners and a degree of common sense prevail.