From the Discord, this list is current as of May 2024. The change log posted here is pretty thorough so everything after that should be on there.

For any mod, you can also go into the workshop mod folder for each mod and check the "missions" subfolder. All mission trees are there in text files named for the country tag (usually).

Current list of countries with Mission Trees:
-Aerie Peak
-Anh’Qiraj
-Amani
-Anga’rosh(Outland only)
-Army of the Light
-Azjol’Nerub
-Blackwater Cartel
-Centaur Marauders
-Drakkari
-Everbloom
-Kingdom of Thaurassian
-Deepholm
-Firelands
-Forsaken
-Golden Lotus
-Gorian Empire
-Gurubashi
-Heart of Fear
-Hydraxian Waterlords
-Illidari
-Khaz Modan
-Kul’tiras
-Kunzen
-Lordaeron
-Nazmir
-Nazjatar
-Withered
-Orcish Horde
-Quel’thalas
-Red Dragonflight
-Redridge Gnolls
-Riverpaw
-Scarlet Crusade
-The Scourge
-The Scourge of Lordaeron
-Sentinels
-Shadowhide
-The Silver Hand
-Silvermoon
-Stormwind
-Stromgarde
-Sunfury
-Tel’abim
-Theramore
-Thorium Brotherhood
-Tideskorn
-Vandelmar
-Vash’jir
-Vermilion Redoubt
-Vilebranch
-Vol’dun Cartel
-Wildhammer
-Windshear
-Winterfang
-Wyrmrest Accord
-Order of Yu’lon
-Zandalar
-Zem’lan Revenants
-Orc Clans
-Centaur Tribes
-Furbolg Tribes
-Northrend Furbolg Tribes
-Gnoll Tribes
-Harpy Tribes
-Murlock Tribes