[Phanx]

I'd use a slightly different approach; rather than trying to generalize everything to the nth degree, I'd just write individual functions for the "special case" addons:

local SavedVariables = {
	["_NPCScan.Overlay"] = {
		["_NPCScanOverlayOptions"] = true,
	},
	["Altoholic"] = {
		["AltoholicDB"] = function(t)
			return {
				["global"] = {
					["options"] = {
						["ShowMinimap"] = t.global.options.ShowMinimap,
					}
				}
			}
		end,
	},
}

local function copyTable(src, dst)
	if type(src) ~= "table" then
		return {}
	end
	if type(dst) ~= "table" then
		dst = {}
	end
	for k, v in pairs(src) do
		if type(v) == "table" then
			dst[k] = copyTable(v, dst[k])
		elseif type(v) ~= type(dst[k]) then
			dst[k] = v
		end
	end
	for k, v in pairs(dst) do
		if type(src[k]) == nil then
			-- "not src[k]" won't work as desired for values of "false"
			dst[k] = nil
		end
	end
end

ExportedSV = {}

function ExportSV()
	for addon, svars in pairs(SavedVariables) do
		ExportedSV[addon] = ExportedSV[addon] or {}
		for name, data in pairs(svars) do
			local svar = _G[name]
			if svar then
				if type(data) == "boolean" then
					-- we want the whole thing
					if type(svar) == "table" then
						ExportedSV[addon][name] = copyTable(data)
					else
						-- not a table, just copy the value
						ExportedSV[addon][name] = svar
					end
				elseif type(data) == "function" then
					-- we only want part of it
					ExportedSV[addon][name] = data(svar)
				end
			end
		end
	end
end

If you really wanted something totally generic, you'd want to factor out the "find and copy this key at any depth" code into its own function that could be called recursively, like the "copy this table" code, but it would probably be more of a headache than it's worth. If you're already writing out by hand which keys you want to copy, it's hardly more work to just write out a quick function that gets the wanted keys and builds a skeleton table with them.

Also, I made a small change in the "copy this table" function; see the in-code comment.