It's common to test new systems on one car before rolling them out across the team. If the technology works and is reliable, Webber will have it before the end of the season.
Every weekend Red Bull claims the two cars are the same and Vettel is not given any advantage. Usually they test on one car in the practice sessions to gauge the advantage it gives over the current car but in quali/race the cars are usually (if we are to believe Red Bull) identical. I find the justification in the article regarding money unlikely though.
Yes, what was not right was the car being in flames because a crash :P
Guess who's had the most issues with KERS in the last two years? Mark Webber.
Red Bull haven't been able to get either the weight distribution or something else right on his car to even get 'normal' KERS working reliably.