There are a couple of scenarios (which may or may not apply in your situation) that I can think of which would create some potential design issues if you want to organize content based on permission/access in this way, which you have already mentioned. My advice would be to limit the display of content at higher levels for role based permission (e.g. admin should only see admin pages, and not admin features on a general user page), and if there are task based permissions within roles they can be switched on or off within the sections of a page.
Keeping this in mind, there are already a couple of alternative strategies used instead to deal with the display of content in similar scenarios (e.g. as used in intranet) that work equally well whether you apply the permission on a role or task basis.
First example is to use a dynamic or data-driven process to determine the content that is displayed. This is not as good for new users, who may be looking around and clicking on different things trying to find what they actually want. However, over time the most used features and most viewed content will be consistently what is displayed. Variations to this type of content display strategy include:
- Recently viewed (constantly updated per defined period of time)
- Most viewed (within defined period of time)
- Pinned items (that persist and overrides the data used to generate the content)
The second strategy is to let the user control the way content is displayed and so there is no surprise or change at all. But how the content is presented to them to choose, and how the configuration is done can all present challenges as well. And this strategy is possible when there is really good IA in place to facilitate an effective search or browse experience.
One other strategy to consider is somewhere between the two, where you can define specific structures or concepts in the user interface (e.g. bookmarks) but leave the organisation of that space to the user (e.g. by allowing them to tag or mark certain content). An example would be the organisation of links in a browser via a bookmark manager that has features like favourites or folders for further organisation.