RiscPkg does not force you to put applications in any particular location. By modifying the path translation table it is possible to achieve any desired filesystem layout. At present this process isn't exactly user friendly, but that can be fixed.
However the recommended method of use is not to worry where the applications are really stored, and simply fake your preferred layout using softlinks of some description.
The next version of RiscPkg will provide a facility for creating softlinks. I plan to support both application stubs (of the type used to implement the Apps folder on the icon bar) and LinkFS image filing system links.
On a more general point, RiscPkg is written (and licenced) to be easily modified, so there is plenty of scope for taking an alternative view of how the filesystem should be managed.
What does need to be fixed in the very near future is the package format, so if anyone has views about this then now is the time to say.
(Draft copies of the policy manual, which contains a description of the package format, are available on request.)