This situation feels like a wrong-footed overcorrection from last month’s controversy.
Last month, Waypoint got into hot water because they presumed a non-consent trope that some trans women find valuable was suitable general-audience material, and suitable representation of trans people as a group. They did not consider the subset of the audience who are pained by non-consent material instead of validated by it.
This month, Waypoint got into hot water because they presumed that a depiction of hurtful treatment of trans women was inherently transphobic. They did not consider that the act of deadnaming could be framed in an appropriately condemnatory manner by a game.
The answer in both cases is the same: presume less, ask more.
As for BotW, the cynic in me wants to chalk that up to that patented Waypoint Sex Positivity; force-femme Gerudo Link is a bit of an online sex symbol, and Waypoint has always been inclined to give a pass to horny.