Removing those pads means you won't have direct contact cooling to the VRM. Maybe try to find padding that absorbs vibrations better?
my understanding is this is typically what causes coil whine, vibrations not being completely absorbed by the thermal pad and/or backplate
interestingly enough EK's new active water block backplates promises to completely eliminate coil whine
They do not promise to completely eliminate coil whine rather possibly lessen whine: EK EXPO | CES 2021: Unlocking the Technology - ekwb.com
Another thing is the benefit of thermal pads between the PCB and the backplate since it reduces coil whine. Thermal pads act as absorbers – they are soft and could lessen the coil whine caused by the vibration of the inductor coils
So could and lessen, no promise of completely eliminating it. As soon completely and eliminate, will open themselves up for people saying misleading advertising etc. But your not wrong on the whole, if you can absorb the vibrations or remove them, all the better to try and reduce whine which in theory the backplate will try to do.