I have a 2005 GC. The number that needs to match is the FCC ID. If that matches and the remote looks the same, it will work. Your comments about having a separate FOB and Transponder key won't work. The FOB/Transponder are one in the same on this car.
I purchased some pre-cut keys from Ebay. You need to be able to turn them in the ignition to get them programmed, so you can't just do what you are thinking of. Here are two options.
Option 1, use as keyless entry only
1. Cut the pre-cut key off of the FOB using a hacksaw
2. Go to Walmart ($0.99) or a locksmith and have a cheapo non-transponder duplicate made of your original key. This will open the door but only start the car for 3 seconds and then it will die.
3. Follow the programming instructions in the manual until it is time to insert the new key and turn it to program it. At that point, use the Walmart key but hold the FOB from Ebay at the end of the key and as close to the lock as possible. If done correctly, the Walmart key will turn the ignition and the FOB will get programmed and can then be used as a keyless entry. The FOB and key are separate things, but the FOB has to be very close to the lock cylinder or the signal it emits will not be picked up. Doing this basically looks to your car just like a normal key. If you pop open the plastic housing, you'll see that the transponder can be removed and will understand how this all works.
Option 2, use as a fully-functional key
1. Do everything the same as option 1, but when you hacksaw off the precut key blade, leave about 1/2 an inch behind
2. Get an extra key cut at Walmart. Cut off the key blade from it also, but do it so that when you line it up with the key FOB stub, there is overlap. The total key length needs to be the same as the original key, make sense?
3. Drill a hole through the stub on the key FOB and the cut Walmart key.
4. Get a pack very small machine screw and nuts (#4-40 x 3/8") at home depot ($0.88 for a 10 pack). They are in a green plastic bag hanging on the wall.
5. Get some epoxy or JB weld at Home Depot or Walmart ($2-$4)
6. Use the screws to secure the two key pieces together, and put the epoxy between the parts to secure it down well.
7. Program this new key using the instructions in your manual. If there is a fit issue, use a file to fix whatever it is. If the key won't insert fully into the lock, it is possible that the stub on the FOB was too long. Again, use a file to file it down.
8. Anyone with basic handyman skills can do this. You don't have to have the epoxy, but without it the two pieces will want to rotate and may loosen up. I just isn't as polished of a final result. I tried this without the screw, but could not find an epoxy or JB Weld that would hold the pieces together. It looked good until you tried to use it in the lock and then the pieces would separate.
Here are some photos:
