I was surmising that CPA timing could be related to number of human controlled planets, but it sounds like no. Ah well, so much for my hunch.
I did a bit of research on the spirecraft scout, since I would not have expected a scout to put a world on alert, but I see now how that could be a very powerful tool. Would have been a great tactic to use in the game described in the OP. We certainly had some mark I and II planets on the other side of the galaxy we could have put on alert, and knowing what we know now that would have been a key strategy for dealing with all our mark IV neighbors.
Anyway, thanks again for the discussion, it's been great!