[Kygo]

You could change the auto loot CVar if you're in a garrison using mapID and zone_changed event if im not completley wrong?
And for the resources overcap, I think MasterPlan has something that does that for resources you can get from missions.

Or try a loot filter addon (if they still exists)

Threw some stuff togheter, I have no idea if it works at all. (took the map ids from Rilgamons post)

local maps = {
    [1152] = true, -- FW Horde Garrison Level 1
    [1330] = true, -- FW Horde Garrison Level 2
    [1153] = true, -- FW Horde Garrison Level 3
    [1154] = true, -- FW Horde Garrison Level 4
    [1158] = true, -- SMV Alliance Garrison Level 1
    [1331] = true, -- SMV Alliance Garrison Level 2
    [1159] = true, -- SMV Alliance Garrison Level 3
    [1160] = true, -- SMV Alliance Garrison Level 4
}
 
local InGarrison = function()
    local name, instanceType, difficultyID, difficultyName, maxPlayers, dynamicDifficulty, isDynamic, instanceMapID, instanceGroupSize = GetInstanceInfo()
        if(maps[instanceMapID]) then
        SetCVar("autoLootDefault", 0)
        else
        SetCVar("autoLootDefault", 1)
        end
end
 
local reg = CreateFrame("Frame")
reg:SetScript("OnEvent", InGarrison)
reg:RegisterEvent("ZONE_CHANGED")

What Fizzlemizz said aswell