Great question — answering as the UphillTech team:
In technical terms, there is little different between the anime on the two source platforms. There are some minor encoding improvements with the steam release, but this is probably not a strict attribute of the content I imagine it is more likely that Crunchyroll has an older version of their encoder on Steam videos in the internal rush to get the partnership out (Purely a hunch, but as a software developer myself, many companies work in a MVP "Minimal Viable Product" release environment, and do cleanup later). Therefore, I would assume that their encoding is likely to change, even if they do not update to their site's encoder, they have a team of developers working on their encoders to try...
Full answer by Toshinou Kyouko: https://anime.stackexchange.com/a/40261 (CC BY-SA 3.0).
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