Did the VDF mention that as well? I know the handbook you're talking is from the 2005 anime. I'm guess you have the ADV release, because I have the three 'Master files' as they call them from ADV's Guyver Volumes 1, 4, and 7.
It's from page 25 from Master File 3:
"SACRED CASKET OF URANUS
These are the fossilized remains of the Creators' greatest spacecraft, located underground of the Chronos headquarters in Arizona. Just three of these spacecraft have been confirmed to exist on Earth, but aside from the one under Mount Minakami, only fossilized remains have been found. It is said that the third set of remains are located somewhere in China's Uyghur Autonomus Region, but details are vague."
The rebel zoalords' base is in the Karakorum Mountain Rang which spans the borders between Pakistan, India and China, That's about 1500 kilometers southwest of Uyghur.
Now since I've been posting and reading the forum, Takaya-sensei has never seemed to be predictable, but I've always felt that his writing has been top notch, not pulled out of his ass. He might be like the famous sci-fi author Frank Herbert. His Dune universe has had an extensive amount of history just for the small amount of novels he has written. I know his son has been co-writing novels of the Dune universe based on the notes. Now if Takaya-sensei makes similar notes to give himself ideas on what to next and he was definitely involved in the process of making the 2005 anime, did he give us a hint about the rebel zoaloads' future plans? Interesting thought, eh? Just wonder if the 3rd ruins was actually mentioned in the VDF?
Now back to the topic, I think the Guyver unit probably have general access to any ship that assigned to the Gaia project. That's probably why Agito could communicate with the navigation spheres of a relic different from his unit's origin. Security probably wasn't tight cause the Advents were the only intelligent beings there anyway.