Hi, I am on vacation right now, but I'll try to review the changes later. Ping me again if you don't hear by the end of February.
Yeah, pretransformed vertices bypass the entire vertex pipeline, that's what they do.
Re depth testing, indeed IDirect3DViewport::Clear doesn't allow you to pass a depth value (that was added with IDirect3DViewport3::Clear2). IDirectDrawSurface::Blt with DDBLTFX_DEPTHFILL could do it, but the meaning of the bitmask is driver dependent, except for zero.