I have been working on a dynamic pane module that allows you to drop panes anywhere without other panes.  During the research on how to implement it, I noticed that any top level div, pane (and IIRC span), that is marked as a runat server, it will assume it is pane. 

Currently, DNN does not allow nested panes, so a runat server block inside a pane should not be found. 

That said though, at some time during the last week I run into a solution that may work better for your situation.  I do not have the location of the message and you might have to search if you need it, but the basic idea is to prefix a custom css file by a role name and inside the skin, simple determine the role of the user and prefix that on a #import statement.  Would seem like a clean answer to change the CSS of a skin (or just even one value if needed) based on a role.

Update: Guess I should have read more, looks like Timo posted just about the same thing.  Although, the @Import of a stylesheet allows you to change any style anywhere on page.