I know that one single Engagement is enough to get fleets done.
or
The Ziggurat uses 50 % CR per Deployment. A Paragon uses only 20 %.
Pick one and let that be your statement. Losing 50% CR not only is not an issue for two back to back engagements if you got 100% (even justv 85) Combat Readiness but it's also
something that does not influence actual in combat performance either.
You optimally want the best ship to command possible for yourself so that you can have the best chance at beating whatever it is you're facing.
Ludd's Angry Broccoli could lose 100% combat readiness each engagement and I would still pick it over the Paragon if it came down to combat performance.
Stick Efficiency Overhaul into that
Moloch-Cursed Abomination if that CR hit really bothers you, but don't let that awfully minor inconvenience prevent you from realizing the fact the Zig is the strongest ship in the game the player is allowed to pilot, in both vanilla and the vast majority of the modiverse that has not completely lost their collective marbles when it comes to balancing their content.
The AI Paragon vs AI Zig discussion I am not going to cover extensively, because it makes no sense whatsoever. A mentally defective child Pather infected by a man eating nanite swarm unleashed by TriTachyon could probably still master the way the Paragon fights while the Ziggurat, being a phase ship, tremendously scales with player skill and tactical awareness, both of which the AI lacks a whole lot of.
I'm really wondering tough, I have not played with the Zig all that much, but what would even be the reason you'd let the AI drive it instead of yourself?
Super ship worth 75DP, unique in the sector, chance of losing it forever? Ah, whatever, give it to Jimmy the Reckless officer with all the wrong skills for it. I want to drive that Overridden Hammerhead instead.