You won't know for sure what is under the top layers until you strip them off.
Like you said, multiple tests indicate cedar shake wood in good shape. However, there must have been some reason why the previous owner decided to cover everything over. Might have spilled paint on a section, might have covered over something? Maybe all done to fix leaks? Simply, don't be surprised to find something once you strip it all down. I would spend the time to do some detective work before refinishing. Try to find out why? Could be the idiot just wanted to put up vinyl. Or thought he would better insulate with the additional layers.
Also, don't forget about protecting from lead-based paint if you have to scrape paint. Wear a mask. Otherwise, it sounds like you want to prep properly.