Not really. Last time I checked: It does provide routines for using .X files, but they're (1) not part of the main api, but rather the helper libraries, (2) completely optional, and in no way prevent one from using their own format. I wouldn't say they take away from the flexibility of DX.

DirectX has built in loaders for X files to load ID3DXMesh objects. Really all an ID3DXMesh object is is a vertex buffer, index buffer, and an attribute buffer (unique ID given to each material/texture/bone/state set) tied together underneath one object. You can load any model format and as long as you can generate those three buffers, then it's as equivalent as loading an X file. Likewise, you can load an X file and from those 3 buffers, do whatever you yourself want with them, which is what I did when I wrote my skeletally animated toon-shading engine in vertex shader language (ID3DXMesh::DrawSubset will overwrite your shader setting in at least DX8.1).