Keep an eye on the other 4Runners that you park next to, guys who steal spares especially ones as hard as underneith the truck know what their doing, and have to specalize in it, the rim/tire both where probably sold for 50 bucks to someone who had a damaged wheel, maybe they will come back maybe they won't.
I know of several people who had spares stolen and somehow they do it, it's hard but can be done.
If you park in high crime areas, just bad areas thats the risk you take, I use to know guys who would get you anything you want for your car, real cheap they had kids do it, I had a cousin who had a TL, they stole the HID 3 times he went to sell it and they stole the HID again, everytime was 4000 in damage, it's to bad they never get caught in the act.
I've looked at the spare and my tools that could cut it down won't fit and I could not get leverage so who ever did it must of figured it out, I'd ask the other people if they ever lost a spare, it's to bad you did not dust the underneith for fingerprints, maybe the person who did it is on record