I ran the same mercenaries guild mission about 4-5 times (starting from out of sector and before the enemies spawned). So I'm reasonably sure the proper scripts were being used, and the way enemies behaved seemed to confirm that. I mostly payed attention to enemy fighter attacks on my destroyer and my fighter attacks on other capital ships.
Under Apollo my Phoenix was constantly bombarded with long range Hornets and Silkworms from all directions. These were annoying but in large part couldn't overcome shield regen. Even without me strafing the enemy rarely fired AHEPTs and the shots never even got within a kilometer of hitting, except for a few turret blasts.
Under Vanilla ships were more aggressive, making HEPT runs that actually connected (or not, depending on my strafing.) They also clearly did the "fire 9 hornets at once" bit, the most I ever saw fired under OCS was 3.
I haven't done comparison test with my Cerberus yet (it's much smaller than the Phoenix, after all) but I'll give it a go at some point.
I like the dogfighting behavior of OCS Apollo a lot, but playing it safe against capital ships is pointless if they don't die.

It could be random bad luck, or it could just be that my Phoenix severely needs a diet. On the otehr hand there were probably about 50-60 enemy ships of all sizes and types and armament generated for that mission, and they attacked from all directions.