According to my research, Project Starcrown was initially nothing more than one of the dozens of questionable war-related projects that sprung up during the late 400s, when tensions arose between Equestria and the Dragonlands after the at the time new, still current Dragon Lord came into power, and it was feared a war would break out as a result. It was, like many of the projects like it, free of any regard for the value of life, and like most of its siblings it never produced any proper results, it was shut down when it became clear no war was going to happen, and everything about it was buried by the Crown to save face.
Unlike most of the secret projects at that time though, at some point newfound interest arose for this one. The original plan was, nevermind the absurdity of the starting conditions required, to implant a mind altering device into a captured dragon to use as a war vehicle. Utter nonsense from top to bottom, but I've seen crazier things proposed around that time.
What's interesting is what they were asking for the second time. It's been hard to find anything concrete besides the name, they hid this stuff a lot better and reportedly everyone who worked on it ended up insane or worse. But all the signs point to them wanting to build a bigger version of the same apparatus Starcrown was designing, or at least something equivalent to that. I don't have the slightest idea why they'd have wanted to do that. There's nothing big enough to stick something like that in, so they had to be planning to use it for something else. But if a crystal cylinder like those was inside the Spire, that would justify the size of the blocks as a way to dampen the overflow of magical radiation and keep the whole thing stable. But what do they need it for?