It's just like I explained here: http://iosgods.com/topic/3161-apple-id-get-modern-combat-5-gangstar-vegas-by-gameloft-on-your-idevice-for-free-no-jailbreak/?p=192406
I have personally purchased MC5 when it first came out and have my account synced and everything. I had to semi-restore my iPad due to an issue with my App Store so I had to reinstall everything including MC5.
I reinstalled Modern Combat 5 using the Apple ID which I used to buy it in the beginning and after opening the game and passing the tutorial, I could see the energy system from the main menu even though I used my Apple ID which had the app purchased.
The game then prompted me if I wanted to restore my old save from the cloud and I said yes and then my veteran rank was back and the energy system was gone (thankfully).
I think any new people who downloads the app from the app store now whether they have bought it or not since the beginning will get the energy system unless they have an account when they were as veteran (before the energy system came).
I could be wrong so you should probably contact Gameloft support for a better answer regarding this. Tell them that you bought the game but still getting energy system.