The flickering itself seems to have been just a display issue, like you suggested, because I exported same as source and ran it through VLC, which showed none of the flickering I saw. The jagged edges are an issue though.
I might’ve found a workaround, which is to open the raw media in quicktime and then use QT to export as 1080p. I both imported and AMA linked/transcoded with that file, and boom! No more jagged straight lines.
Just as an experienced opinion, though, do you think quicktime is a reliable converter? Not sure how much trust I should put in it…