Well the intricacies of Section Access are not very easy to explain. At the risk of not making myself particularly clear, here goes:
If you use Data reduction based on section access ,and there is a connection between section access and section application, then the resulting data set after data reduction will determine whether a user is granted access. No data remains after data reduciton = no access.
If you use Data reduction based on section access, but there is no link between section access and section application (because of being commented out), then the section access table will only be used to look up users with access to the document. Data reduction will not have any effect.
From your second post I get that the login window doesn't appear when you try to open the document in the AccessPoint? It only appears when you comment out the Load of the link values in Section Application?