To check if the rattle is from the spare tire or the tools (jack, lug wrench) just remove them
all from the trunk, drive over a rough road (or rough surface) and if the noise persists, you'll know to look elsewhere.
Suggestions: look for a loose exhaust/taillpipe, often caused by a broken hanger allowing a pipe to bang on the underside of the vehicle - or a loose bumper bolt rolling around inside the steel bumper (under the plastic cover). It could be almost
anything - and, as metallic sounds usually 'travel' throughout the vehicle - it may not actually
be in the rear of the car. Finding the annoying rattle may take awhile - and the use of a lift. Be patient.