Pass 3 Key System

My Pass 3 Key system is not working on my aztek.

The dealership said it was because of my autostart and will not cover it. That I have to pay 500 something dollars to fix it.

I was wondering two things:
1. Could the autostart have caused it?
To me it didn't because my car died with the key in the ignition and I pulled it out to give it jump (done it ten times before and noticed that if I pulled the key out the Security Light would come on, and if I left the key in (or never put it in) and jumped it, the light would not pop up.

2. Is it necessary to have the pass 3 key system working? Will it affect my car in the future?


Thanks