The odd cutscene with Y'shtola and Runar in 5.3

[MoofiaBossVal]

We hear an odd, tinny sound when Y'shtola talks

My thought was that it was actually the Sound coming back and that the Scions were more sensitive to hearing it than everyone else because of the loose connection between their body and soul, but given how we haven't heard the Sound since 5.3 I'm guessing it might not have actually been it after all.

My understanding is that the Sound is coming back right now.

In 4.5, you had Matoya's magics shorting out. A few people I've talked to have attributed that to the Light aether from the First, but light aspected aether shorting out magic is not an effect demonstrated in the story. What is? The Sound. at the end of 5.0 we learned that the Sound warped the magics the Ancients used.

Then, in 5.2, Urianger heard a sound which ruined his water walking spell. In 5.3, Alisae and Y'shtola hear the Sound as well. These incidents are distinct from Thancred becoming tired due to his soul being divorced from his body.

As for Y'shtola retiring with Runar on the First: that'd be nice, but I don't see how it could possibly happen. The story has been very clear that moving your body between shards is pretty much impossible. The Scions, Unukalhai, and Clyva were only able to go to the First as ghosts (and FFXIV has been inconsistent on that: the Scions were fading away as ghosts, but Ardbert, Unukalhai, and Clyva weren't. I guess maybe they have the echo and that allows them to stick around as long?). Not even the Ascians are capable of bringing their bodies on the Source to the First; Emet had to possess some random sob and reconfigure his physique, and Elidibus possessed Ardbert's body. There are only two characters in FFXIV who were able to bring their bodies over to the First: the Crystal Exarch (by riding the Crystal Tower, using a huge amount of aether to do it), and the WoL (due to really wonky writing that makes the WoL the one exception). Unless the Ironworks are able to recreate the time travel/dimensional transporter and install it in the Crystal Tower and allow Y'shtola to use that to go to the First, there is no way she is able to get there.

And besides, Y'shtola's is said to have been burning up her life force by using her eyes to see aether. Or at least, that was a line dropped when she started using her eyes to do so and it hasn't been brought up since, so it kinda feels like a cheap excuse that didn't mean anything in the end. I'd sorta like for that plot point to be cashed in and for her to fall ill or pass away after 6.0.