This place raises more questions than it answers. Let's actually dig into some weird fucking lore and timeline shenanigans.
>3,000 years before Generation V:
>The Relic items are created.
>3,000 years before Generation VI:
>The Kalos war occurred, the ultimate weapon was created underneath Geosenge Town, and AZ was given eternal life. This sets a chain of events into motion that leads to the discovery of Mega Evolution.
>2,500 years before Generation V:
>The Relic Castle is built.
>The Dragonspiral Tower is known as Unova's oldest structure, though its age is unstated.
>1,500 years before Generation I:
>The earliest known system for writing is developed and used at the Ruins of Alph, Tanoby Ruins, and Solaceon Ruins. Archaeologists are currently unsure whether the nearly identical Unown preceded or succeeded the writing system, but it is assumed they share some sort of connection.
If we look at the timeline, shit starts not to make sense. I threw in the Ultimate Weapon story because I find it amusing a weapon of mass destruction is older than written language in the Pokemon world. Now I'm not saying that the Abyssal Ruins are 3000 years old, because having a relic that's 1500 years old isn't unusual, look at the Japanese Imperial Regalia for an example. Now we might assume that the Abyssal Ruins were built at the same time as all the other ruins, and that could make sense. But on the other hand it was likely created after the Original Dragon split, given the version exclusive runes. It doesn't help that GF didn't give any specific time for it like all the shit that went on 3000 years ago. Maybe you could make some inferences about the architecture, if somebody's into that. If it is similar could argue it's GF re-using assets/tilesets, but Zelda theories have been built on less so it's probably fine.