Most people aren't experts. If I'm setting up a bunch of churches in a line to make a point, I'm doing it to make a point to the vast swath of common people in them, not the handful of experts.
You have made the assumption that the line-up was done for the sake of human people, whether common or expert. When choosing the site to build a religious facility, would not the sake of the deity(s) being worshiped be a primary consideration?
Only the experts of that time could have found out that this churches are all lined up according to the Meracator projection, if they had any idea of that projection at all. It seems rather as if your top-secret St. Michael's conspiracy, which, without leaving any written traces, when carrying out its secrete plan over several centuries using advanced cartographic and geodetic knowledge to determine longitudes, was aimed at the mystery-susceptible people of our times.
That's not necessarily true. I recently read Barnabas Calder's Architecture: From Prehistory to Climate Emergency which contains several mentions of the incredible detail architects put into their work- from ancient Greece through mediaeval cathedrals. Details and design which would not have been noticed by any eye but an expert's.
I'll try to look up an exact quote later. But the gist of several passages was that there was an elite or expert community- obviously, or nobody would have been designing buildings like this!
Let's assume for the sake of this discussion that the 7 sites are deliberately aligned by somebody. They would presumably be a powerful elite, and would be doing it to impress other powerful elites.