SE started out adding MIDI to the Model D.
Then they started building their own Model D’s with MIDI built in. Those were indeed clones.
Then they started adding things to the basic 3-VCO-and-a-ladder-filter architecture of the Model D, essentially ending up building their own family of synths with their own ideas, way of working, and sound.
Don’t forget that all creative work builds on top of the work of others. Nobody in the history of electronic music has ever created anything entirely original, entirely new that was in no way at least inspired or partly based on something else that came before.