Understand your idea.
We have been discussing this back and forth when we were implementing the private pages functionality. The reason we ended up deciding to keep all member-only pages under one node is usability for members. In this way member when he logs in can easily see what private pages are now available to him. If they were spread out, member would have to go through the whole site (and few people would ever bother to do it - this is actual feedback we had from many administrators who were using such functions in other systems).
A secondary reason was also to keep admin interface simpler. Now to make a page member-only admin simply moves it under member-only node. Otherwise each page would have to have an option Public/Private and we always hate to add options into interface since it confuses many less experienced users.
We know that there are still other pros and cons and we do plan to introduce more flexibility in this area later in the year.
Your feedback - and a very detailed and comprehensive description is highly appreciated.
Dmitry Buterin, Chief Apricot