Usually we do section access script at data model side and then later doing binary for data model into final layout.
Even if u are doing section access than you are doing already restriction on users , authenticated user from QMC will not work here. Application will be distributed based on section access.
Amit is right. Section Access can be combined with "Distribute to authenticated users" to simplify the creation of a QDS task. You'll never have to worry again about distributing to Named Users, because in the end Section Access will reduce the list of authenticated users to those that appear in the Section Acces table.
Section Access always has the last say, because it becomes active at the time a document is opened, and not when a document is reloaded/distributed.