Yeah, it's definitely possible that the town has been dug up again. But then the question is when does MiB enter the church? Is that supposed to be a flash forward from his current storyline?
That's just in the present timeline that he's always been in. Teddy was told he would find "Wyatt" where their story started, and he replied "Escalante." So, MiB knows where to go when he frees himself from the horse noose.
EDIT: Just to clarify, there are three timelines:
Before the park opens (30 years ago and some change) - Arnold and Ford are living in the park while testing and refining the initial hosts in Escalante. Arnold and Dolores have talks, Ford and Arnold have a falling out, Dolores kills Arnold, Teddy shoots up Escalante, which is buried.
30 years ago, park is officially open - Logan and William visit the park, William falls for Dolores who is becoming self aware due to Arnold's conversations before his death.
Present - Ford introduces "reveries" into the hosts, allowing them to gain new phsycial behaviors based on past experiences. This triggers various malfuncitons among hosts, and Maeve and Dolores to becomes self aware, causing the former to plot her escape from the park and the latter to re-live her experience with William from 30 years ago. MiB (William) is trying to find a deeper level to the park that he believes has been left by Arnold, and is funneled into Ford's new storyline while accompanied by various hosts, namely Teddy. Delos is trying to wrest control of the host code from Ford, who still has the upper hand due to the code only being on site and Ford effectively being a god in total control in the park. Theresa is killed by Ford/Bernard after it's discovered she was attempting to send data outside of the park using satellites, Elsie is seemingly killed when she gets tangled up in things, Bernard becomes self aware due to Maeve's probing and is seemingly decommissioned by Ford.