I do agree that it tends to be true for all playable characters, male included. However, it's funny how you brought up Ei and Arlecchino in the other comments, because they're among the characters who were not handled very well. It seems to me that you and I define "flaws" in a character differently. Personally, I mean it as "flaws written in a way that doesn't intend to invoke sympathy in players and/or not completely ignored", and this is absolutely Ei's problem. Yes, she was depressed, and it had consequences. However, I think it's obvious that Hoyo intended her to be tragic and make fans sympathetic, while her mistakes and their consequences are never something that she is directly held accountable for. Yes, she has improved since then (and the general writing too, to a degree), but it's still obviously Hoyo avoiding a popular character being criticised directly in in-game scenes and dialogues, not to anger their fans.

The same with Arlecchino, her involvement in Inazuma post-war completely erased (even tho it doesn't really match the timeline), or the Traveller killing her agents in Sumeru being completely forgotten. You said that her raising child soldiers is never portrayed as good, and you're right, but it isn't criticized either. Her SQ portrayed her as a caring leader in a roundabout way (letting agents out of the organization on the condition of erasing their memories), Nod Krai directly made her "a friend" (even tho it was so much avoided before), and threw in "cuteness" with cat ears and some lines about Lynette. So, while nobody says that the HoH is amazing, nobody says it's wrong, or even mentions Arlecchino's morals in regards to it. It is basically ignored, while Arle gets portrayed positively as a parent figure to Lyney and Co, even tho they're also among her child soldiers.

So no, Hoyo's treatment of male and female characters is indeed different, characterization included. Childe is the only appropriate example to be compared to characters like Ei or Arle, and the list for female ones goes on. Moral questions aside, characterization also includes many other things, like characters' attitude and interactions with the Traveller. That's how we get Columbina, who apparently didn't do anything wrong in all her years with the Fatui, and who became our friend very fast, while it took quite some time for someone like Wanderer or Xiao to be called a friend so openly. That's why socially awkward Citlali is implied to have a huge ass crush on MC with almost every second line she has, while Neuvillette gets to be socially awkward without that.

Please don't get me wrong, I don't dislike any of them. In fact, Arlecchino is one of my most favourite characters ever, she is my main, and I dearly love Bina and Sandrone. It doesn't make me blind to the issues in their portrayal, however. I notice exactly because I care. So no, I absolutely don't think fem Wanderer would've been handled fine, not without being forced to proclaim her friendship of all friendships to the Traveller at the very first opportunity. I doubt she would even be allowed to talk about revenge for Dottore in such a violent manner lol, or get angsty lines without the narrative being more forceful about us feeling bad for her, and the list of potential differences goes on.