Earlier quoted context omitted.
I think that FSM does satisfy your stricter definition of counterculture. Like the Church of Satan, one of the stated goals is to force legal examination of whether or not "freedom of religion" actually means "freedom to practice Christianity". LARPing and kink also have some opposition by fairly mainstream religious-types. They're seen as counterculture, even if they don't define themselves that way. Sorry. Changing…
Maybe the FSM is counter cultural but only in the way that housecats and lions are both felines. There is a very large difference between trying to hang Mike Pence or kill police and believing that established religions are illogical. Maybe it's slightly countercultural in the areas where Christianity or other religions predominate (which is not where I live).
And yes, both lions and housecats are felines. There's gradients and degrees. I'd call the folks you're talking about as "extremists" not a mere counterculture.