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The reason anons shit on "indy joshi" sayers is because when many people here started watching, corporate joshi wasn't really a thing. It was all "indy joshi." Nor is it a designation used in Japan itself.
Samurai TV has two shows - one called Joshi Puroresu No Oshigoto (Joshi Pro Wrestling's Job) and Indy No Oshigoto (Indy's Job). Sometimes these are translated as "Occupation of the Joshi" or "Occupation of the Indies." The indy show covers men's wrestling, "indy" is never used as a word to describe any joshi company.
As pointed out above, it's also not useful as a designation of which companies are drawing well and which aren't. Greybeards have seen many popular companies fall and many small companies rise.
TL;DR - It's a lazy, counterproductive phrase used by foreign fans who don't know jack shit about the subject matter.