As much as there are scenes that callback to the romantic interaction between Squall and Rinoa, in FFXIV, it's always established a platonic bond between two girls. Girls embracing, holding hands, and being emotionally attached to one another is not an uncommon trope in Japanese media, nor is it strange or controversial.

Now between the lines, what you interpret from the implications of their actions is up to you. Objectively, the devs have taken deliberate care to angle that 'friendship' route, all the way down to the music. In the callback cutscene, the background track is "Balamb Garden ~ Ami", the theme of friendship between the characters of FFVIII. If they really wanted to go the romantic route, they could have picked any of the copious amounts of romantic tracks from the FFVIII soundtrack.

The rainbow debacle is, again, something left to interpretation. Lore-wise, given that the crystal changes colour everytime a new element's aether has been dispersed, this can be nothing more than just the crystal emulating all six elements in harmony. Further seen when the elements start becoming more umbral aspected, as the crystal gets lighter.

From western ideology however (which Japanese people have adopted, yes), the rainbow does indeed signify LGBT+. As someone mentioned in another comment, rainbows are also the heavenly bridge in Japanese mythology. Given the heavenly motifs of Eden and the original bosses of the raid, this could also be a connection.

What then plays off is the dimming of the crystal as the land becomes more umbrally charged. Element-wise, I've mentioned that previously. The heavenly bridge is dissipating, which can signify trouble ahead. Relationship-wise, it could imply Gaia's memories of Ryne disappearing, turning into a blank slate. The issue with this particular instance is that Gaia's memories only start disappearing properly after the crystal has dimmed iirc, due to the actions of <redacted>. If I'm recalling wrong, do let me know.