Welcome to Bike Forums. I am going to go out on a limb here and suggest your problem is too much gel padding. It sounds counter-intuitive, but sometimes with contact points (saddle and bars), less is more, as the gel does all of the wrong things under pressure. The GRX hoods are arguably the best ergonomic design out there. I have Ultegra, which are a close second, and I have found zero-padding gloves (and a leather saddle) to be the most comfortable. It might also be an issue of bike fit, meaning some very minor tweak, like a shorter stem, might really be what is needed.

To answer your question, you can get gel stuff that can be cut to shape from Bontrager and other manufacturers, and you could probably put that between the hoods and the inner portion of the brakes/shifters, but it ain't going to be pretty.