Hi - thank you for the report! Took a look, and it seems like - when it's not under threat - the Ziggurat uses phase cloak reasonably while retreating, it never builds up enough flux to be slower than if the cloak was off.
... come to think of it, that's actually unlikely in the first place - the speed will at worst be at 1/3rd of maximum, while the time acceleration is 3x. So this might be a marginal issue when the zero-flux boost is factored in (assuming the ship isn't firing), but if the ship is under enough threat that it had to stay phased that long and couldn't pull away in that time, it's very likely to have been in trouble anyway, hmm.