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In the standard version, fractions didn't cause any issues, and everything was calculated correctly.
Fortresses won't be weaker if, in addition to the 50% increase, they also provide a one-time bonus of +50% on tiers 1-2, 1-4, and 1-6, if that dwelling exists.
As for upgrades, they should be designed to compete with fortresses and basic dwellings in terms of priority. A +100% one-time increase is great, but in my opinion, it should also include a +50% increase in creature production (on tiers 1-6).