You assume it was an intruder. But why do you believe that everyone else will make that same assumption?
I have come home and found my garage door open a couple of times. But I don't assume that someone broke into my house. Other people live in this house. They may have left the door open for a reason. I also know that the cat sometimes runs into or out of the garage while the door is being closed and that triggers the safety circuit and reverses the garage door opener.
Amanda didn't live in the cottage by herself. She had three roommates that could have left that door open while they stepped out for a minute. Or forgotten to lock it when then left. Finding the door open was a bit odd, but not a reason to call the police immediately.
That doesn't work. Knox knew that Laura and Filomina were away from the cottage that weekend. That left only Knox and Meredith that may have left the door open. Knox knew that Meredith left before she did at 4pm on November 1, so Knox was responsible for locking the door when she left on November 1.
On the morning of November 2, Knox knew that Meredith was the only person that spent the night at the cottage, that the front door (not a garage door) was wide open, Meredith is no where to be found, there's blood in the bathroom, there's a bloody footprint on the bathmat and so what does she do? Knox leaves the front door unlocked, has a shower in the bloody bathroom and is not at all concerned.