Kyouko x Mami is canon.
Really? When was that confirmed?
Canon is a tough argument to get into, particularly since it's constantly changed by time travel and universal law rewriting. Official is a better word for it, since their pre-Homuloop backstory is highlighted in the the third drama CD, the PSP game, and The Different Story manga and is Urobuchi-approved.
Different Story is a spinoff of the series. The writer who wrote the manga said that "Different Story" was a "what if" story of Mami hadn't died. Also in the anime Kyouko doesn't seem to show any sign's of sadness or heartbreak when she learns of Mami's death.