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"...
Counterpoint: the Salamander short story is just the starting condition of Koyuki and Konatsu's relationship and not meant to be its end state. In the first chapter, Konatsu tells Koyuki she reminds her of the salamander from the short story, to which Koyuki replies that she doesn't think she's as stubborn as the salamander. Then in chapter 14 Koyuki muses about how the salamander and the frog should've been more honest with each other and changes the "I think I've had it" line with "I wish we could always be together", making her own interpretation of their relationship (and her own relationship with Konatsu) explicit. Since then she's been trying to figure out her own feelings towards Konatsu and Konatsu's towards her. To me there's been a clear build-up towards a clear resolution rather than leaving it up to interpretation. Whether that resolution will be super friendship (which would personally feel like a major cop-out to me at this point given how the characters act and many other situations that have occurred) or romantic is a different matter.
Also, this was my very first post, I guess. Hi all.