I have been seeking the answer to this very same question for a very long time. Many years, in fact.
Many sources state that the village and the church were built specifically for the film in, or near, Cuernavaca, Morelos, Mexico.
However, I have never been able to confirm if they still exist, or not.
Frankly, I doubt that they do. They certainly are not a part of any Mini-Hollywood type theme park.
As far as I know, the only theme park in Mexico that is somewhat similar to Mini-Hollywood is "Villa del Oeste" in Durango.
An amazing amount of films have been shot there, from the 1950's until the present day.
Since part of THE MAGNIFICENT SEVEN was, indeed, shot in Durango there is the chance that the border town set (the one where McQueen and Bryner meet and organize the Seven) was there.
However, I have been told that set was in a different location altogether.
We may never know the definitive answer(s), amigo.
You probably already know this, but here is a link to the list of locations for THE MAGNIFICENT SEVEN via IMDB:
It isn't much help as it is a non-specific list.
However, it is a good general reference.