MS had a rigorous certification and internal testing process, new D3D versions came out quickly to support new hardware features, and through the Xbox Microsoft had more real world experience for what games actually need than the GPU vendors themselves, which probably helped to rein in some of the more bizarre ideas of the GPU designers.

I don't know how the D3D design process worked in detail, but it is obvious that Microsoft had a 'guiding hand' (or maybe rather 'iron fist') to harmonize new hardware features across GPU vendors.

Over time there have been a handful of 'sanctioned' extensions that had to be activated with magic fourcc codes, but those were soon integrated into the core API (IIRC hardware instancing started like this).

Also, one at the time controversial decision which worked really well in hindsight was that D3D was an entirely new API in each new major version, which allowed to leave historical baggage behind quickly and keep the API clean (while still supporting those 'frozen' old D3D versions in new Windows versions).