I don't know if she was or not, I do believe her or her body was in there in the RAV4.
Whether you believe Brendan's story or not, he and Avery were in there cleaning with bleach, gas and kerosene the night she disappeared. His own mother stated the same.
I don't have any earthly idea why Avery would lift the battery cables, but he did. His DNA that wasn't blood was right there where Brendan said he opened the hood and lifted cables.
Do you really think someone snagged her just as soon as she left Avery's, before she could make any calls. Murdered her, snuck into the Avery compound and hid the vehicle, planted Averys blood, scattered her bones? Do you understand how many things would have to fall in line perfectly for that to happen?
And if you believe the police planted the key then you must believe they killed her too. How else would they be in possession of the key?
How did Averys sweat DNA get on the hood?