yeah the spire end fleet triggering all sorts of stuff can be quite deadly I imagine. Yesterday I finished a 7/7 Raid engine game with alternate ending. The spire fleet was triggering raid engines and counter guard posts everywhere. I can imagine this to be lethal at higher difficulties. The alternate ending SHOULD always be a win, no matter with what settings you play.
I can say quite soundly, that even with the exo transcever on one end of a 120 planet snake map, the AI warp counter attack posts in 10/10 5 homeworld game can and has destroyed my home command stations after about 4 hours of running. To stop it, I basically have to move my turret ball there, and allow the endless waves of ships to hold the front point.
Other annoying things they do is manage to get the AI up to 50,000 ships of threat, yes, ships, from deep striking. Needless to say, my computer was crawling at that point. Throw in the fact that I had waves incoming from Warp Counter attack of 24,000 and a CPA of 7,000 incoming... I think I was getting close to 1 second of game time per 4-5 seconds wall time. Before I activated them, I was doing fairly close to 1:1.