[Alan Anderson]

Originally Posted by Jonathan Norris

In my interpretation the Coopertition bonus is totally separate from the seeding points, it says nothing about adding the Coopertition bonus to seeding score in the rules. This is where I think I may be wrong, someone please correct me if so.

You quoted it yourself:

Originally Posted by 9.3.5 CoopertitionTM Bonus

All teams on the winning ALLIANCE will receive a coopertition bonus: a number of seeding points equal to twice the un-penalized score (the score without any assessed penalties) of the losing ALLIANCE.
In the case of a tie, all participating teams will receive a coopertition bonus of a number of seeding points equal to twice their ALLIANCE score (with any assessed penalties).

The bonus does add to seeding points.