I sincerely doubt this as some sort of random or unknown issue. It uses the exact same attach points as a stock cooler or even a good aftermarket cooler. None of those warp the mobo or gpu. Keeping the temperature extremes down should prevent warping, if anything. I’ve been through two WC motherboards and 3 gpus and have experienced zero warping.
The only thing I can offer is either the boards that do warp are cheaply made and unable to support the weight of a good waterblock or the installer is over-enthusiastic about securing it and does so too tightly and thereby causes the damage. My current waterblock has specific instructions regarding installation to prevent over-tightening and damage to the motherboard and components. IOW I suggest it’s an installer problem the vast majority of the time.