Crunchyroll started as low quality speedsubs, their strategy was being the first to release the latest episodes of shows airing at the time. Alongside speedsubs you had quality subbers which would release a couple days later with higher quality translations and using better RAWs. Crunchyroll quickly became the dominant speedsubs, always being first, so eventually you had CR subs too. These would improve CRs shoddy subtitles a bit, maybe add character colors and formatting and such, and then release shortly after.

Yakitate Japan only started streaming on Crunchyroll after having been officially licensed by Nozomi Entertainment. They almost certainly used the official subs rather than doing their own.