Hi there. I personally believe that there is no safe phase till our PPR. But chances of rejection due to missing documents etc. decreases (almost eliminated) after IP1 changes to NA i.e when your R10 check is done. Then during NA stage your eligibility, criminality are being checked, so if you are confident that you are a good citizen (which most of us are

) and you have provided sufficient evidence of your eligibility, i.e work, education etc. you can consider yourself quite safe.
About the later question I have no idea what happens inside CIC offices, or how they function, all we can do is speculate and assume.
In my opinion it is not possible for them to employ so much man power to scrutinise reference letters in a manner as to understand what they mean in say professional terms for each and every profession out there if that is what you mean, but then I also believe that they have sufficient experience and access to professional analysis, if needed. They check everything very minutely, IMO, and have sufficient skill and experience to understand if something is fishy or missing no matter the technicality involved in the NOC of the applicant. They generally don't go to many lengths to verify information if they feel everything is in order, but once a doubt arises they can investigate as much, they have access to lots and lots of information at their hands.
P.S- This my personal understanding and opinion and is in no terms reflective of actual procedures, its my own assumption from my research.