Why does that bother you? There are multiple things Dolores are seeing. The town with the church is a testing area during the beta before the park opened. It is where they first trained the hosts. Something happens there and Arnold dies. Ford literally buries the town along with its secrets and opens the park to the public. Dolores feels drawn back to the place, and William is the one who actually takes her there, but they don't get to finish their journey. She remains trapped in her loop for 30 years until MiB returns to reawaken her. And she starts following Arnold's calling again, retracing her steps, but because she is remembering now, as she journeys through unfamiliar territory her only anchor is the one time she traveled it before - with William. Her memories are triggered by people and places she has encountered before in the past.
We know that in the entire Arnold storyline, Dolores is the lone witness left who knows exactly what happened. She is the last person to speak to Arnold before he dies. So it is already established that as far as what the show would need to show us eventually, there are these events. There is no question now that William's story is happening in the past. We have factual confirmation from the show that he is in a time that is inconsistent with the present. Ford already dug up the town.