New rear hatch wiring different than original?

Long story short: I got hit on the freeway on the rear end, and the hatch needs to be replaced.

I purchased a used 4th gen rear hatch that was in decent condition on ebay. I noticed that the original wiring in the vehicle only has a single 12-pin pigtail, I believe 9 pins are being used. However, on the new hatch, there are 2 pigtails coming off of it, one spliced onto the other. The larger one is the same 12-pin male clip, but more pins are being used, I believe 11 in total. The smaller pigtail that runs off the larger wire is a 5-pin, with only 2 or 3 pins actually active. Ill upload pictures.

What's the recommended approach? Would there be an issue leaving the smaller pigtail disconnected? Would there be an issue with the newer male 12 pin connecting to the existing 12 pin that considering the difference in active pins?

 

What year is your current 4runner, and what year did the new hatch you bought come off of? Maybe there are differences in years for the hatch (like how there are differences in 04-05 headlights/taillights compared to 06-09). Did your 4runner have the spoiler with brake light on it? I wonder if that 'new' pigtail is for the brake light or something.

 

My 4runner is a 2003 SR5, and the new one came off of a 2005 v8.

 

Hmm, looking at photos of each year, they both have a top of hatch brake light (whether its on the spoiler or not), both have the wiper mechanism, both have rear window that moves up/down and both have license plate lights. If you have a multimeter maybe you could test the smaller pigtail when you press the brakes or turn on the lights to see if its related to either of those.