so even if they have 2 tokens assigned they wouldn’t take a click because they are unable to assign a 3rd? I get that nobody can have more than 2 but my understanding is it would function like incap in that case and they would take a click, similar to colossal stamina

The reason Incapacitate deals damage when they already had 2 tokens is because the ability explicitly says it deals damage. It has to do so because of the situation described; that a "3rd" token can't appear and damage is not given.