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 to get maximum performance out of their servers (this caused some backlash when Crunchyroll degraded quality substancially in the past).
For comparisons of image encoding, see this Reddit thread.
There are a few licensing differences between streaming via a Crunchyroll subscription and purchasing a title to stream on Steam.
The most significant of which is that a purchased title will not expire. Often Crunchyroll will expire titles that are underperforming in exchange for newer titles. When you purchase a title on Steam, you do not have to worry about this happening.
Also of course, you do not have to pay recurring payments to keep access to your titles.
Thanks to @Peilonrayz for pointing out that Stream releases are also censored.
I believe the partnership with Steam is mostly a strategic move by Crunchyroll to develop a dual pricing model of their services. This can be seen also with the introduction of their Manga Store, for manga that are unavailable with their subscription.
Partnership with Steam also gives Crunchyroll access to a significant target market. Anime and Gaming overlaps significantly.
I imagine that this is mostly driven by growth goals set by investors and demand from publishers - Similar to the Spotify or Youtube model, streaming does not net much money for a series per view ( Crunchyroll claims counter to this, but has not provided figures to date ) - however, if titles are sold individually they can net much more. For larger series in particular, this is a much more lucrative option.
I imagine that in the future we will see this pricing model develop further.
TLDR: There is not much difference than the way you would like to pay for the content. This move is more motivated by investors and producers