You know Konatsu is a Tokyo Girl when her profile pic is her with a dog filter
Jokes aside: now that I read "The Salamander" (anything for the yuri.), I feel like I can finally give my opinion on the manga. And honestly I think the "Subtext" tag can't be anymore accurate of what the manga does...
I really like the many references to Ibuse Masuji's short story - though it feels like it's completely based on it when it comes to Koyuki and Konatsu's relationship. (Sorry if I'm about to repeat something that was already said in the previous comments)
Long story short (though it's a short story.), "The Salamander" allows the reader to interpret the salamander and the frog's relationship however they want. It doesn't set in stone what they think of each other at the end of it, only their dialogues and actions are written down. This is pretty much the same here. We have countless "flags" of Koyuki having her friendship with Konatsu going over 9000, but it feels like the Yuri Goddess swore to secrecy until one of the girls actually say something directly. That, and the lilies blooming in the background.
So honestly, even if it's frustrating, it feels like the author just wants to give the same freedom of interpretation as "The Salamander"...
... and then Kaede turns out to be the main love interest, that'd be perfect