I will point out here, as I did for the OP when they approached me at NRaas at about the same time, that all TS3 mods are package based content, not just those from NRaas. They are no more complicated or any easier to install than any other package based files, and as such do require the Mods\Packages Framework to be in place first. How granular one might want to get with their configuration once they are actually in play depends on the mods and the player's preferences.
The Downloads folder is for content to be installed by the Launcher. Package based files cannot be read or worked with that way, that's only for sims3packs.