You are free to upgrade a Mac Pro or Power Mac without automatically voiding your warranty.
But, they do have a clause in there that the warranty is voided if they determine a defect to have been caused by the end-user, or by the additions and upgrades installed by the end-user.
So, if you install the video card yourself, and it develops a short that damages your computer, then Apple would not cover the repair.
But, if you purchase the card from Apple, and pay Apple to install it, then you would be covered under warranty if damage were to result.