Very good post +1.
Some additions / minor corrections - HIRV (Human I.. Rights violations) and misrepresentation are also checked along / after security check. Some late refusals are caught at this point too.
Also, any change in circumstances that occur AFTER submitting actual application (which only brings down CRS score, will NOT result in recalculation of score) as long as an applicant meets the MEC (minimum eligibility criteria) for the PR program itself (not Express entry but either FSW, CEC etc.) e.g. if some one gets married after eApr and hence loose points for spouse if he was to submit application now, this does not result in recalculation of score, nor does leaving an LMIA job. However, if for instance your language test scores turned out flawed or your experience found is incomplete / in sufficient for the PR program (1 year full time for CEC etc.), then yes this would cause a refusal.
Lastly, the R10 okay review is the actual stage which used to be AOR before the current Express entry system. Some time back until CIC required AOR for a BOWP application, it was actually this R10 okay, which was needed in order to be eligible for BOWP.
But a few months ago, considering faster processing of EE, CIC has allowed any applicant to submit BOWP application if needed, ALONG with the PR application. It will automatically be processed, once your R10 is passed. Of course, this comes handy if some is left with 4 months or less in current work permit validity and wants to submit BOWP along with PR.