mw13, why are you ignoring the question: Do you think the CC held that Rabbeinu Tam and his kehilla were mechallel Shabbos? Because you clearly imply so. A simple yes (or no with an explanation on your discrepancy) shall suffice.
The prohibition that melacha is forbidden after shkiya is undisputed. The machlokes is over when shkiya is. Rabbeinu Tam has a shitta that is held by large portions of Klal Yisroel. The reason “it is a possible prohibition punishable by stoning” (di’ho safek issur skilah) is due to the uncertainty whether Shabbos starts at shkiya or at tzeis. (And since it is uncertain, everyone agrees we must start Shabbos at shkiya, but not all poskim agree when shkiya is.)
Now please address the question posed to you.