That seems a very confusing and limiting method. Most frameworks use the PEAR naming convention which makes it VERY easy to place files wherever you like as long as its on the include path.
Controllers, views, and models however are likely to require there locations to be configurable, though I guess it depends on the framework. Some frameworks prefer convention over configuration which usually makes them easier to use. You simply force users to do it your way. However, force to hard, and users will break the rules, hack your framework, or move on to something less restrictive.