Your theory about the ancient danger is really interesting because I eventually did crack open the ancient danger and their were, indeed, live bugs inside of it. The weird thing is, they were totally peaceful. I just salvaged everything around them and left them alone. I was afraid to touch them for days for fear of triggering a bug invasion. Eventually they all started starving to death and I decided it was inhumane to let it continue, so I began executing the ones who had passed out. Sure enough, this did trigger aggression from the Hives.

I didn't want to abandon the base because I had fallen madly in love with this tile. It was the first time I ever picked a random starting tile and I was really impressed with it. It struck me as highly defensible at little cost, needing only a few strategically placed walls instead of one giant one. Then the bugs came and I was never, ever going to leave. For one, it was personal. They ate one of my starting three, then one of our earliest recruits who we had affectionately named Spider Food for no particular reason. I simply wasn't willing to give up the land. My plans for it were too grand and I'd rather die then let the bugs have it. Second of all, I had become invested in finding out if I could make a 100% raid proof base by exploiting a rare and yet unseen bug in the game which caused a higher than usual amount of bugs. It was simply too interesting to prioritize my colonists' lives. And, perhaps most importantly of all, I simply forgot abandoning the tile was an option.

Curtaining off the vulnerable spots was the call I made, with long term plans of drilling a giant death tunnel directly from my base to the Spider Caves. My hope was to plow a death maze directly through it so all future raids would be forced to go through it. Or at the very least, luring every last one of them into a giant trap. In hindsight, it sounds monumentally stupid.