From everything I've read, the alibi theory/narrative is predicated on the prosecution's timeline. Bobby Dassey sees Teresa taking pictures at his uncle's residence at 2:30 PM, he takes a shower, and then sees Teresa and his uncle walking towards his uncle's residence between 2:40-2:45 PM. Phone records demonstrate that after 2:41 PM, Teresa's phone is never used again. Blaine Dassey sees his uncle place a plastic bag into a burn barrel, he subsquently sees fire coming from inside the barrel at 3:46 PM, and he doesn't see Teresa's vehicle on the premises. Avery then calls Teresa's cell phone at 4:35 PM.
The prosecution postulates that if Teresa was alive between the hours of 2:42 PM and 3:46 PM, she would have had her cell phone with her and she would have used it in some form or fashion. The fact she had not used her phone by 4:34 PM raises the question as to Avery's rationale for leaving a 13 second voice mail message? If Avery wanted to schedule another appointment, why not broach the subject with Teresa when she was on his property? I believe he felt safe calling her cell phone two hours after she arrived at his property. Avery had already destroyed the cell phone in his burn barrel, so he knew that law enforcement could never prove the context of his voice mail message.
IMO, Avery initially thought he could use this 4:35 call as a way of distancing himself from Teresa. For whatever reason, he decided not to mention the 4:35 call to investigators and he went with the following narrative... She came to my property, she took pictures of the van, she give me an Auto Trader magazine/bill of sale, and then she drove away a little while later. Avery had to think fast because he had no idea when Teresa would be reported missing. Ergo, the destruction of her body/personal belongings, cleaning the garage with bleach, and moving/obscuring her vehicle in a matter of hours.