WMG / Infinite Space

Yuri and Kira's Incest Subtext is a result of a case of Platonic Writing, Romantic Reading on the part of the Overlords

The Overlords, being Eldritch Abominations, obviously don't get humanity very well; they just know that Kira's not on board with staying with Yuri and doing her Tracker duties. So they Hand Wave it by making Kira extremely attached to Yuri (and vice versa). Not getting how humans actually interact, this makes their relationship start to look suspiciously romantic in character, especially because Yuri and Kira were not actually together in early childhood (because they didn't have an "early childhood"), and so wouldn't be affected by the Westermarck Effect. So, because the Overlords didn't check their work very well, it becomes another bit of "stuff gets extremely weird around Yuri," which ends up negatively affecting their plan when Yuri and Kira rebel.