[Nitram Draw]

For the Tech trees you could put all the standard techs in a separate trait with no cost. Then if you did not choose this trait you could never use any tech from it.
This would allow you to modify all the standard races to get the tech without affecting the points in the game.
The Pirate could not use this tech. I don't know if there could be a flag to disallow choosing both Pirate and Standard trait but if there is a way, you would solve the problem. Of course the Pirate tree would have to be fairly large if you wanted a lot of variety available to the Pirate.