[Slakah]

Too my knowledge :

local PocketPlotDB = setmetatable(PocketPlotDB or {}, {__index = defaults})

is the same as

PocketPlotDB = PocketPlotDB or {}
local ppdb = {}
setmetatable(PocketPlotDB, ppdb)
ppdb.__index = defaults

The only difference is that in the first method PocketPlotDB is local, so I'm guessing your "PocketPlotDB is nil" error is due to variable scope. i.e.

function printvar()
   print(var)
end
local var = "cat"
printvar()

would print nil.

As for your other problem of the metatable not being applied to existing substables, you could do this:

local function DeepMetatable(tbl, defaulttbl) --I couldn't think of a better name
    for i, v in pairs(tbl) do
        if type(v) == "table" and defaulttbl[i] then
            DeepMetatable(tbl, defaulttbl[i])
        end
    end
    return setmetatable(tbl, {__index = defaulttbl})
end

local defaults = {
    color = {
        r = 1,
        g = 0.6,
        b = 0.6
    }
}

PocketPlotDB = {
    color = {}
}
PocketPlotDB = DeepMetatable(PocketPlotDB or {}, defaults)
print(PocketPlotDB.color.r)

Would output 1.

Whereas the other

PocketPlotDB = setmetatable(PocketPlotDB or {}, {__index = defaults})
print(PocketPlotDB.color.r)

would give you nil.

I think the reason why the previous method I posted didn't work because the __index metatable wasn't applied to pre-existing subtables, so if those pre-existing subtables were missing values there was no __index metatable to get the default value.

Hope this helps.