The increased pre-travel is consistent with the dampening pads getting squashed. The shorter rubber pad means the stems sit higher up when not pressed, so they have to be pushed down further before they reach the actuation point.
Unless elasticity can be improved, I suspect this is always going to be a tradeoff with silencing performance. The softer the pad is, the better it is at silencing, but the more easily it gets squashed. If you make the pad harder/stiffer to resist getting deformed, then it won't silence as well. However, if it's possible to use a rubber with better elasticity, it can be soft and also keep returning to the same shape after more presses.
But I bet the switch manufacturers already considered these material properties when they selected a type of rubber to use, and they aren't going to suddenly find a better material just because we ask them to. They can't just use the best material theoretically possible--their choices are limited to rubbers that are 1) compatible with the machines and manufacturing processes they use, and 2) available at a competitive price from suppliers. I'm sure if there was a better rubber that met both of those criteria, they would probably have it by now. I'm just some guy. You can bet a professional manufacturer has put more thought into it than I just did.