You should only need to have the ECM flashed before installing it in your WJ. Unless your SKIM module lost your VIN there should be no reason to have the SKIM or keys reprogrammed.
The SKIM and PCM not only verify VIN, but also exchange the secret SKIM/key code. When a PCM is replaced the SKIM needs to know.
When you take it somewhere to be programmed its really not even the PCM you're flashing/programming, it's the SKIM. The code is something only a dealer or someone with acces to Jeep's DealerConnect website can get.
Excerpt from FSM:
PROGRAMMING THE PCM
The SKIS Secret Key is an ID code that is unique to each SKIM. This code is programmed and stored in the SKIM, the PCM, and the ignition key transponder chip(s). When replacing the PCM, it is necessary to program the secret key into the new PCM using the DRBIIIŽ scan tool. Perform the following steps to program the secret key into the PCM.
1)Turn the ignition switch to the On position (transmission in Park/Neutral).
2)Use the DRBIIIŽ and select THEFT ALARM, SKIM, then MISCELLANEOUS.
3)Select PCM REPLACED (GAS ENGINE).
4)Enter secured access mode by entering the vehicle four-digit PIN.
5)Select ENTER to update PCM VIN.
NOTE: If three attempts are made to enter secure access mode using an incorrect PIN, secured access mode will be locked out for one hour. To exit this lockout mode, turn the ignition switch to the ON position for one hour, then enter the correct PIN. (Ensure all accessories are turned off. Also monitor the battery state and connect a battery charger if necessary).
6)Press ENTER to transfer the secret key (the SKIM will send the secret key to the PCM).
7)Press Page Back to get to the Select System menu and select ENGINE, MISCELLANEOUS, and SRI MEMORY CHECK.
The DRBIIIŽ will ask, “Is odometer reading between XX and XX?” Select the YES or NO button on the DRBIIIŽ. If NO is selected, the DRBIIIŽ will read, “Enter Odometer Reading (From I.P. odometer)”. Enter the odometer reading from the instrument cluster and press ENTER.