I have been wondering which of those formats is \"best\"? Schema.org, Microdata, and RDFa are bit of a pain to implement. They can break validation and require quite an effo
The lines between Microdata, RDFa, and JSON-LD are indeed currently very blurry and that there is still no widely accepted de facto among the three. This will have to wait for now. Perhaps a couple or more years.
Meanwhile, Microdata should not be labeled with Schema.org like you mentioned because those two are different things. Schema.org is a vocabulary so it can be used for Microdata, RDFa, and JSON-LD.
Using Schema.org as the vocabulary and using JSON-LD as the data representation is probably the most anticipated pair because of two common aspects about them:
but even so there are still disconnects between the two like this example.
Regarding the JSON-LD support, since Bing, Google, Yahoo!, and Yandex acknowledges the use of schema.org then perhaps it is safe to say they are also supporting it like in this example.
Google has been very pro-active in promoting JSON-LD-schema.org these past couple or three years.