I think Rincewind means in terms of intelligence. Also, in game terms the Trolls are slightly easier to play (at least in the beginning, not sure about later on), but because you switch sides that doesn't matter.

However, I think the point Pterry was trying to make was that these two species have so much experience in fighting and hating each other that in game terms they are equal to each other. Skill at the board game is derived not so much from tactical savvy as from the ability to think like a dwarf or a troll. On the Discworld, anyway. That's why the best Thud players were the ones who immersed themselves in the other culture.