"works fine" is very different than "is equivalently optimized."
Valve has done a lot of work to get games to work well on the Steam Deck, and that likely translates to other AMD GPUs. So it makes total sense that Valve would optimize the Proton translation layer for DirectX calls to the AMD driver differently than the NVIDIA driver (or rather, in a way that AMD handles better). A big issue in GPU optimization is keeping it busy, so perhaps the AMD driver working with Valve's patches on the DirectX to Vulkan layer improve utilize m utilization. That could translate to a modest performance improvement even on well optimized games (perhaps 5-10%, probably not more than 20%).
I don't know if that's what's going on here, but it's a plausible explanation.