If you revisit the timeline and click on ALL the respective phases you’ll get an expanded detail. When you click on the Multi Engine phase you’ll clearly see the ME and MEI ratings are in fact included.
Also to clarify the stages: its Instrument, commercial Single engine, CFI, CFII, Multi engine add on, MEI. Once you get commercial single, you are a commercial pilot. The multi checkride is adding multi engine to your commercial pilot certificate.
Same goes for instrument. You get an instrument rating in a single engine plane. You will shoot approaches during your multi add on to be able just add multi engine to your instrument rating.