As someone that was in the fandom when the series first began its run in 2014, i watched this as it was coming out, they essentially had a Soul Eater moment which is why things were changed in the anime (ie the anime adaption started production way before the creator was finished with the manga.). 2014 was still a VERY rough time when it came to queer people, but it is Yuri. Every single character in this series is canonically lesbian and one of them even has two fathers. Additionally, the creator has made doujinshi that expands on the characters and their relationships with each other. It is all canon since it was made by the creator of the series.
I watched the anime a while back and I didn't see any real yuri relationships despite the genre. They just kinda seemed like really good friends in the anime. I know sometimes the studios dial down the gay in anime adaptations so maybe its better in the manga? I just wanna know if the main ship is canon cause I'd rather not read it if its just queer baiting. (づ￣ ³￣)づ