No, Miller cycle engines can be both naturally aspirated or supercharged. The misunderstang is due from commercial matters, Toyota named Atkinson his first Prius engine to distinguish it from some Miller supercharged past engines. If you read universitary books of mechanics, you can immediately understand the difference between Miller and Atkinson.
Till now we've only seen n.a. Miller on hybrid vehicles like HSD and supercharged Miller on standard cars, as the actual Note and Micra with the 1.2 Digs. The problem is the low power and low torque of N.A Miller engines, nobody would buy a 1.5 16v with only 75ps... Now some Mazda's and Honda's engines, using peculiar materials, desing and strategies, can switch between Miller and Otto joining both efficiency during normal driving (where the engine runs in Miller mode) and power when you deeply press the gas pedal and the engine switches to Otto mode. The technical problem is knocking, because old petrol engines could not run on Otto Cycle with 13,5:1 of Compression Ratio, but a 10,5:1 RC is good for Ottos, not for Millers... Now Honda and Mazda can do it, look at this:
http://www.mazda.com/en/innovation/technology/skyactiv/skyactiv-g/They don't say the Skyactive runs in Miller Cycle, but with low power request it runs in Miller mode variyng the camshaft timing.
