I agree with the OP. Its not just the build menus, its the "You cant evolve so close to the enemy" ones, and the "you cant build on this surface" ones. If I am alien and i hit the evolve button and then a human moves into range, i try to evolve, but no luck, i have to close 2 windows before i can move, and often, i am dead by then.
EDIT: One solution, would be to put non interactive messages in the chat. They appear for a few seconds in some bright and noticable color, and then fade. That way, you dont have to deal with the popups.