Strange, I use modsetting.json to give IX Battlegroup (From Emergent Threats/IX Revival) some station Augments, but their High-tch Starfortress have only 32 MAX AP?
Some Trinity World's Battlestation have 30 AP, but one have only 22 Max AP, too.
Besides, if you add some markets in modsetting.json from mods you didn't activating, all NPC station augments will go missing.
For examplt: Give "eis_chitagupta" (from Iron Shell) "SA_heavyArmor" and play with Iron Shell, all is good. Then keep these setting and play new game without Iron Shell, every vanilla station Augments is lost.