Just dropping in here, but it's definitely easy for someone to look at female sidekicks in video games and see a trend that lines up with the portrayal of female characters in media in general. That said, I think a lot of what this video (and some of the other ones) points out might also have to do with some design and tech challenges.
One theme I see permeate through this whole series is really, the inherent lack of agency a fictional, AI-controlled character will have. The player character is the sole character who gets to "control" things. Games like The Last Guardian where sidekicks have a degree of autonomy are rare and the tech behind making that work is probably still quite primitive. Yorda and Elizabeth open doors all the time for the same reason your squaddies open doors in shooters -- because the function serves as the bookend for all the stuff the player does. Everything AI characters do has to serve the player's experience.
Firstly, it might be interesting if we got more games where AI characters acted a bit more independently of whatever the player is doing. Skyrim is a popular example where you often find characters, male and female, going about their routines and sometimes getting into fights that are totally unrelated to what the player is doing. Action sequences where AI characters freely fight each other and actually do things beyond what he player is triggering are nice too. The alternative in a linear game is to put the player on tighter rails while the sidekick sort of acts as a cut scene, taking agency away from the player. Secondly, we probably need more games with ensemble casts of player characters. Maybe hot-swapping between characters should be explored more. In general I think video game stories might open up if more of them took multiple perspectives.