All a notary is doing is validating that the person signing a document has a government-issued photo ID that matches the name under a signature line. Nothing more than that.
Agreed, though there are copies of the documents made and given to all parties. If a document is changed after being notarized it can be proven in court what the original documents contained. A real notary will be tracking the number of pages, making copies of all of them and signing off what they witnessed. Everyone gets the signed copies and everyone provides their ID in person. A full chain of custody is simply not possible using internet based services with current technology.
I'm pretty sure when I've gone to a notary in Massachusetts, they've just checked ID, witnessed a signature, stamped the document, and made a notation in a log book. I'm pretty sure they've never made a copy of anything. There is something called a Medallion Signature though which perhaps involves more.