I would not have an issue with them. The rules do not clearly state is legal to replace the shift boot. It does say you can remove interior trim carpet, etc.
So in many respects the stock leather boot and rubber one are "interior trim" in my definition of the word. So you cna remove. I suggest keeping the rubber boot to limit under body fumes/heat from entering the car. Even so I would not have any issue with a person replacing the stock rubber shift boot with a fireproof material.
I also can't see how any tech offical would see an issue with that.