Every single DirectX powered game will use some sort of .X model. The .X framework handles meshes, any type of mesh that the engine needs to support. So even if you store your model in some obscure format, when you load it in the chances are it becomes a standard DX mesh format.
I guess it depends on how you look at it though - the principles are all the same when using an engine like DX, it expects meshes to be handled in a specific format whether you do that directly or not. Animation and texturing is usually handled differently by pro's than how we would deal with things - which is why they don't just opt for the standard .X format usually. Thing is - we have these options already, we could take our .X models and convert them to DBO objects which is a lot more like the techniques the pro's would use. One aspect is protecting the media - how freakin awesome would it be to root around games like HL2 and find a load of .X models!.
Another reason why pro's might keep this extra layer of abstraction is that if they stick to their own model format and just convert over when loading, well they have full control over what their file format contains but more importantly the media is transportable between platforms and engines.
