If going by the letter of the law (so-to-speak) then yes, it should. Majority of companies let it slide as long as you're decent enough to restore it back to factory condition before RMA-ing it. S'why you're starting to see companies selling Graphics Cards with waterblocks prefitted by the manufacturer... too many RMAs due to folks killing their cards whilst (clumsily) fitting a block - which would generally result in either damage to the GPU Core, or missing components around the core and on reverse by the mounting poles.
good article, although what you said kinda contradicts it
saying that though, if i install a block, and it breaks itself irrespective of that, then putting the stock cooler back on and RMAing it stands fine with me