I thought I'd share my strategy.

Mykara Heroes have Retribution Damage really early. So what I did was
1. Level up hero by taking out minor factions to get that Retribution damage a.s.a.p. Once Retribution damage is maxed, max his +1-3 food per exploitation skill, then his +15 security skills, then +5% FIDSI skill. AI never declared war on me. I'm guessing it's because they think they'll lose to my retribution damage. I had a Necro in the game.

2. Fungalize all strategic resources and completely ignore Faction Quest.
3. Era I is the same as every other race. During Era II+ prioritize Fortification damage first, then dust, then industry, then science, then influence, then food.
4. All pops into science unless building important buildings like Museum of Auriga, Industrial Megapole, etc.
5. Buy Science Stockpiles and pop them one at a time after unskilled labor.
6. Turbo Fotios. I got that tech turn 110.
7. With 3 Fotios, I can steamroll the entire AI army, and I did. I took their Urkans and wiped them out. Watch out for expansion Victory. Fotios had his +3 range weapon (total 6 range), and the Free Counter accessory. Amassing these strategic resources was hell.
8. After getting 3 Urkans, use their Tremor to take out fortifications, and 5 Fotios to steamroll everything. I won. Supremacy.

Any tips on making this better? Was I correct that the fortification damage prevented AI from warring early with me?

The list is vast. I suggest you check out the changelog here.

There is a more general sense of what the mod does on the mod page.

To give you an idea of one of the things it does is allow the AI to pursue and complete quests. These were auto completed for the AI in vanilla and in terms of the faction quest NEVER completed.