Maybe HP/Defense/Initiative/Fire Damage Bonus (whichever it is) = essence + (Fortress training level - 1).

Anyway, I'm sure the Stardock team could explain it well.  Having this feature just makes it a much tougher choice between Conclaves and Fortresses for high essence cities.  And really, Fortresses should be the best at training very powerful military units, with or without magic help.

Wait... why do you automatically go conclave with high essence? I try to have one high-essence fortress for exactly that reason: so I can crank out good units with those bonus-per-essence enchants.

What am I missing?

Well, I never build more than one fortress, but I always build one.  If you check my .982 AAR, Stables is the native fortress, and at the time it became one, it was my most essence rich city.

As for multiple fortresses, at this point, I do not see the necessity. I believe in few, but elite troops, and I'll never have the crystal/iron income to build more than one per turn. (I usually save Gildar before I reach tech milestones, and rush my troops)

If the new release makes arrow fodder indispensable, I still won't need a second fortress, I'll just build chaff wherever. 

And anyway, I don't build troops unless I can build ass kickers, and once I have ass kickers, fortresses become quite plentiful... By turn 142 in the AAR I have two non-native fortresses at 0% unrest.

actually i started turning my high essence locations into fortresses and my low essence ones into conclave, simply because i don't want to train my units out of conclaves and i need an ideal of 4 essence to crank out fully enchantes crack troops (troops on crack or whipcrack tough, you're call).

You only need one essence to really ge the conclave bonuses going since it's really about the research bonus rather than the enchantments.

conclave ==> research

fortress ==> training

the food one ==> err food, and gold.

I'll use a high fortress troop to make damage dealer elites, and a second fortress to make meatshield, or anywhere else to make the meatshields as required.

Since the fortress level bonus doesn't agree well with henchmen, i train my henchmen at a high essence conclave town. I willfully take full advantage of the bug that gives them free accessory bonuses so i can get a big helping of fire/ice damage boost to their range attacks while they level up.