Well, here is an update. I did get a new headliner btw.
Took my car in Saturday at 8AM. Dealer called at 4PM and said it was ready but they broke some parts in the back so they would be ordering new trim pieces to fix that. I get there and they are having trouble with the Intelligent Access. They were trying to reprogram my key, replace the battery, you name it. Somehow in replacing my headliner (which looks good again Yay!) they completely disabled the ability for my car to sense the key fob. The lock and unlock buttons don't work even. It was 5PM on Saturday so they gave me my crippled car and sent me on my way.
So for now I'm taking apart my fob every time I want to get in my car. The thing they don't tell you is that you have ~10 seconds to start your car before the thing goes totally crazy with its car alarm. So 10 seconds from unlocking the door to get into your vehicle, reassemble your fob, jam the sucker into your steering column, hit the brake, and then the start button. I've given up on reassembling the key fob as a step.
All I know is that if they rip out my headliner they better put yet another new one in to replace it or I'll be at square one. Maybe I'll try the dealer 5 minutes from my house in the future instead of the one where I bought the car. haha