Recommendation: Do not use Transport mode (makes things harder). Disconnect the negative terminal from the battery, and put a good AGM tender directly on the battery.
How to open the trunk with a dead (or disconnected) battery when the car is locked (for verts, and ZLEs when the secret-back seat release isn't opened in advance):
1. Remove the plastic cover on the stationary part of the door handle on the driver's side (notice the slot on the bottom). Make a note of how it comes off, see Notes below. Can be pried off using a key, but better with plastic trim tool to reduce scratching/damage. Remove the metal key from your fob and unlock the car.
2. Get in the car and open the hood with the release under the dash.
3. Connect a 12V power source to the jump terminals under the hood. Wait 30 seconds for computers to wake up. Pop the trunk using the fob. If the key fob doesn't work, hold the start button down for 6 seconds with foot OFF the brake pedal to put the car in to key-ON mode. Then push the trunk button on the driver's door.
NOTES:
- If you put the car into transport mode before it lost power, the BCM & Key fob, as well as trunk release may be disabled. So you will have to get the car out of transport mode via jump-start before either will work.
- If the car is low voltage (say from external 12v source charging the battery if you did not disconnect it), the BCM may not allow the trunk button to work right away. Charge the battery using a proper AGM tender/charger for a few days.
- Reinstalling the door handle cover must be done the way it came off (rear end first IIRC), or it will get stuck half on and is a pain in the ass to fix.
- If you removed the battery from the car, use it in step #3 above.