Both versions don't use native sprites. They generate meshes based on the data and therefore don't have any problems with FFD. But that said, they work fine when mixed with native sprites in the same scene.
The main difference between them is that 2DToolkit handles packing the individual image parts into its own atlas, whereas the plain Unity version uses the libGDX format and a pre-packed texture.
Note that FFD hasn't been officially implemented yet in any of the runtimes other than libGDX but there's a functioning repo fork of Spine-Unity with FFD in github if you want to try it out.
They're hoping to get the Skinning feature working in the editor and libGDX before officially implementing it in the other runtimes.(I'd say Unity will be one of the first to get it since C# is incredibly similar to the java/libGDX runtime.)
