I have seen that and it is very frustrating to have these words.
But look at what CIC says is needed for BOWP.
And also see this further down on the same page.
Taking these together clearly implies that the 2nd AOR is conclusive proof of program eligibility. Look at it this way, EE is fully online. The system does not let you submit without uploading every required document. So the eAPR is just confirmation that the application package is complete - of course it is because that's how the system is designed!
And the 2nd AOR is sent only after someone went through your documents and confirmed that you have uploaded relevant documents which demonstrate program eligibility and not a series of cat images or Justin Bieber lyrics (Do note that uploading Bieber lyrics might get you barred for life, even in Canada!).