Ok, took a look, and yea, the main problem is that your first hub has been up for nearly 10 hours and your second for something between 3 and 4. Remember how the journals were warning you that the AI wasn't going to like this?
I don't think 20 hour games are going to work well with the Fallen-Spire progression no matter what I do, unless I just totally gut the challenge.
That said, this next coming version will cut back a lot of the excessive accumulation of the counter for you, but in the future please understand that the AI will kill you if you send up flares like those cities and then wait that long
I mean, what's it supposed to do, just wait for you to build up a big Spire fleet and come kill it?
And yes, following the progression into the multi-city phase does make it likely that normal ways of attacking an AI homeworld become much harder or impossible. Should you succeed in following the progression further, however, victory is possible.