Ask from @wolveragrace!
THEY WERE EXTREMELY SLOW BURN mostly because Estinien quietly pined over Seren/Rifra ever since he was freed from Nidhogg's grasp. In my headcanon (as seen in some of my gposes) Estinien develops draconic features (such as reptilian eyes and black scales throughout his body), and his resulting Halonic guilt is what sets him off on his own journey during Stormblood. He saw himself as a monster, ravaged by a vengeful wyrm almost as if it was his punishment for being consumed by his own vengeance, so for a long time he felt like he couldn't be by Seren/Rifra's side. Of course, they meet during the Stormblood Dragoon lvl 70 quest and post-Shadowbringers, but it's thanks to Krile and Tataru's constant nagging that he finally allows himself to join the Scions.
Rifra, however, doesn't really notice his feelings properly until after their one night stand in Thavnair, looking back at how Estinien seemed to always be where she was with the Dragoon lvl 70 quest and Ghimlyt Dark (not to mention him destroying a magitek cannon). On top of that, she herself started developing feelings for him during the Garlemald arc, realizing that he was a kindred spirit like her for many reasons. She considered confronting him about it during the Andron inn room scene, but with the Final Days looming over them she decided not to.
It's at Ultima Thule when they finally share their own feelings for each other. Right before Estinien disappears, he turns around to Rifra to confess but is cut off before he could say anything. When all the Scions return, he immediately runs to Estinien, holding him tightly in an embrace.
Rifra then does the same thing when he teleports the Scions away right before the Endsinger fight. He begins telling Estinien "If I don't make it back from where I've gone, just know I-" but the teleporter finishes before he too finishes.
And here is where they finally confess! There's too much to explain in that fic that I can share in a Tumblr post so I recommend reading it!