I don't think they would have locked it and how did they get the keys? They didn't break in because TE has said there was no damage to the car. And no alarm went off, or someone would have heard it.
Heathers keys are STILL missing. TE had to use his spare keys to drive the car home. If she was jumped at home or in parking lot they'd have her keys.
I think the somebody would have been LE, or her father, or both, and that would have resulted in a stolen car report for which there would be a record and a statement by now.
Except we don't know Haethers history of car use-did she do wahtever and did she disappear or not communicate for days at a time?
I can see what you're saying about considering other scenarios, but I don't think this one is plausible. Heather would have been screaming if/while still alive, and her body would have drawn attention long ago if placed in one of the environments you suggest.
I'm confident this is a very sad case of a person or persons known to her deciding for vindictive reasons to lure her and end her life.