Are “canon” and “megatext” synonyms? If not, how do they differ? Are they related?

Yes, they are related, but they are not synonymous. They are both used to describe SF and other genres, but they are based on different perspectives. A megatext is outlined by authors that contribute to certain themes and sub-genres by creating alternative and derivative works from each other. A canon is outlined by the general community on which individual works contributed to the overall culture of the genre.