Does the QT launcher download from trunk of FGaddon?
With some 24 hour offset, for better or worse it does. The packages which the launcher ships are re-generated every day or so by a script fetching trunk from FGAddon (which might mean that the aircraft downloaded doesn't actually run on the last stable version because it was changed after the release and uses core features currently in development - that's why 'for worse'.
Any other aircraft downloaded by means other the launcher can simply go into a separate directory and the launcher told about it in the relevant tab. If there's a name conflict (because there's stable and devel version of something installed) the order decides - I think first directory in the list wins.