I think the 4Runner uses two antennas. One on the tailgate, the others on the two side cargo windows.
The extra wire is very important! It is the antenna booster/amplifier wire for your 4Runner. When I installed my HU, I did not hook up the smaller black wire and my radio reception sucked.
I then read over the wiring schematics for the 4Runner and found that I needed to supply it with power. I spliced attached it to the Power Antenna wire on my AVN5435. I think it was a blue wire, but I am not sure.
Once spliced, my radio reception was much better.
IIRC, only one of the antenna plugs fit in my HU. I did look for a Y adapter, but was unable to find one. So I guess I am down an antenna compared to the stock 4Runners.