Can that paywall killer get you into members only sites such as Ancestry.com or is it just for MSM sites, and how does it know the difference?
No
It only gets around 'soft paywalls' - which used to be most of them. The Wall Street Journal just implemented a 'hard paywall'.
Bookmarklets are mostly JavaScript which only modifies YOUR computer - they do not touch anyone's server - which is why they are legal.
Many paywalls work by giving you a 'cookie' - this thing deletes them all, thereby resetting them.
Or it reroutes your path to the magazine, like for FT - it sees that you are trying to read FT; grabs the title of the page, then reroutes you through the FaceBook referrer, where you can read the article free!