The way I'm thinking about things now is that the Shurimans got the Sun Disc or the means to create the Sun Disc from Mount Targon, and that the disc ties in with one of the planes that intersects with the mountain. The denizens of Icathia took it one step further and began exploring the possibilities by which they could open new gateways and junctions to other planes of existence, but in doing so they actually made the Void intersect with Runeterra where as before the two didn't meet at all.
In doing so it weakened the walls between the realities and allowed for a large scale Void invasion, which was only quelled when the Ascended of Shurima and the Aspects of Mount Targon joined together and led a bloody campaign in to Icathia, where probably thanks to Bard or something they stitched up the gaps in reality and stabilized the situation, but they couldn't completely separate the Runeterra and the Void, so the two peoples instead had folks scour the land and be prepared to tackle any void related shenanigans. With the decimation of the Lunari, the Solari enclosing themselves around Mount Targon and the collapse of the Shuriman empire there was no one left to keep check of the issue, and so the old wounds between Runeterra and the Void widened, allowing Voidborn to once again appear in the world.
I feel like the reason Mount Targon has void problems just like Shurima is because all planes that intersect with Runeterra also intersect with Mount Targon as sort of a convergence point between the planes. Soraka's Grove might be connected to somewhere in Ionia specifically but it can just as easily connect to Mount Targon. In that way when the Icathian's brought the Void much closer to Runeterra than ever before they also linked it to Mount Targon. Of course that's all just me speculating like a madman.
Also as a note for anyone who doesn't actually know what cyclopean is in the context of buildings, it's basically stone of varying sizes roughly fit together with no mortar work. It looks like this:
http://images.fineartamerica.com/images-medium-large/cyclopean-masonry-michal-boubin.jpg
It's more indicative of primitive building practices more so than otherworldly construction. It was likely used by lovecraft initially to give the impression of truly ancient construction by beings that didn't grasp such ideas like proper masonry as we'd see it but were still capable of making immense buildings and structures despite this.