Suppose for the sake of argument that one of those template gurus is correct and that all great screenplays have an underlying invariant skeleton of X beats. The implication (what sells books* and seminar seats**) is that writers must have Template X as the “structure” of their stories in order to be successful.
If you gave Template X and the same brief synopsis to ten writers who know the basics of the craft, you’d end up with ten different stories — most likely some bad, some good, some in between.
Although all ten scripts would have the same underlying invariant template, each would have its own structure, much as two songs with the same chord changes will probably have different melodies comprised of different patterns, e.g. rhythms, tempos, harmonies, phrasing, etc. (not to mention different lyrics).
A script has many different structures, and the underlying template (assuming there is such a thing) is probably the least important. It’s certainly the least distinguishing characteristic, the factor that by definition can’t set the story apart from other stories.
Story IS structure if you include all the various patterns that the writer creates (pacing, callbacks, subtext, archetypes, thematic development — there may be 10–20 different kinds of structure in any particular script); i.e. “story is structure” means “story is the sum total of all the different structuring elements.” It’s why writers should read scripts (plural) not just the most typical example of a particular template.
The danger of the Template Guru approach (even if there were a single correct invariant template for all successful scripts, which I don’t buy for a second) is that it encourages writers to ignore the most significant elements of structure — the elements that the writer creates by choice rather than by obedience. Technically, it’s not the use of a formula that causes formulaic writing; it’s the ineffective use of the non-formulaic elements.
* “The last book on screenwriting you’ll ever need” shouts the cover of Save the Cat. Unfortunately, the publicist who wrote that tagline didn’t know that Blake Snyder would go on to write two other books on screenwriting.
** Those seminar ads that list “successful alumni” don’t cite the tens of thousands of people who have followed the guru’s advice without writing a successful screenplay as a result.