I thought this might be helpful, given that settlement customization is much more extensive and meaningful in FATW: DoM than in RTW Vanilla, or even previous versions of FATW. At the moment, it's still WiP and I may have gotten some stuff wrong, so please correct it if that's the case.
There are spoilers here, so anyone looking for surprises in campaign - consider yourself warned.
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Diversification
Dwarves
Elves
Adûnabâr
Dale
Dunland
Harad
Reunited Kingdom
Rhûn
Rohan
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Resources (all factions, including minor ones)
Two tiers each (after choosing an industry via the "rights" marker)
Construction
Animal Husbandry and Fishing Rights
Estates and Farmlands
Precious Materials
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Dale only: Engineering
Bonuses of consecutive tiers are cumulative (meaning there is no downside to upgrading windmills or ploughs)
Inventors' Workshop
+1 Happiness bonus