Oh wow, Youko is the worst and reminds me of every single straight girl that led me on in my life (so I might be extremely bitter to those types). Youko's wish-washy-ness of her feelings with both Yae and Ayumi just tells me that at the first sign of problems, she'd probably run away or go with the safer option (hence the beard ) and I think someone like Ayumi deserves better than to be the side thing that she is.
The Yae and Chitose thing will be fine, I feel like because of the prequel we know they'll be endgame. Chitose also has mentioned multiple times that she loves Yae the way she is and Chitose likes the way she is as well. Yae is just insecure about Chitose being in an environment she's never been in and might be too naive about it (i.e. guys hitting on her and doing something sketchy without her even realizing it). I do think it's kinda redundant since I feel like they've went over this multiple times in the prequel but what can ya do ¯_(ツ)_/¯