You are right, there are a lot of things that don't make sense if Avery was the killer. Why he wouldn't clean the RAV 4, use the kiln/car crusher, or kill her for that matter is beyond me.
As an investigator in law enforcement though I constantly run across people who think they are a fucking all-star criminal who will never get caught. They cut corners and get complacent. How they conduct their illegal activity whether it's robbing a bank, distributing child porn, or kidnapping someone is mind boggling and never well thought out. Often times it make no sense. But for some reason they think they are the shit and will get away with it. They are never thinking three or four moves ahead.
Him not cleaning up more thoroughly/making better decisions really isn't surprising to me at all. What does catch my attention is the ineptitude of law enforcement to search the premise in one sweep. How they could call a mulligan multiple times on a search warrant is beyond me (and then find evidence).
Regarding your third point. It is quite alarming (if he did in fact kill her) that he is able to act so natural during the media interview. He is engaging with the interviewer and isn't deflecting any questions or fidgeting. Definitely looks like an innocent individual.
^^^Edit: Was it that there were mysteriously deleted messages or that the ex-boyfriend couldn't remember if he deleted any or not?