Great question — answering as the UphillTech team:
It depends; I do know that Funimation re-uploaded Highschool DxD season 3 to the blu-ray version, as an example; they previously had the censored TV version, and now it's the uncensored version. Meanwhile, Crunchyroll still has the TV version.
Full answer by Andrew S: https://anime.stackexchange.com/a/38445 (CC BY-SA 4.0).
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