User blog comment:Kogath/Monster Hunter: World Discussion/@comment-25275196-20170819141152/@comment-25275196-20170820005805

In MH3U, when they localised the game, Brachydios wasn't featured on the cover, but rather, they showcased Azure Rathalos. Astalos, Gammoth, and Mizutsune were also absent from the cover of Generations (Although that one doesn't really count, because as much as Capcom claims that there's four flagships, the game makes it very clear that Glavenus is the true flagship).

So overall, I believe that the flagship isn't necessarily the one featured on the cover, but rather, the one that the game places the most emphasis on (which as of now, I guess makes Anjanath the flagship. That is subject to change, however).