The question is how to characterize these "few cases". I assume for now, that the "few cases" can be characterized as a type of application, therefore subclassing the xowiki app (like in s5) looks appropriate. i would do the following way:
1) subclass xowiki::Package as ::myapp::Package
2) in mayapp-procs.tcl, define in addition to ::myapp::Package the class ::myapp::MyWikiForm with the intended methods (use "next" in the methods to chain to the default behaviour if necessary/intended)
3) in the method initialize of ::myapp::Package, make a "::xowiki::MyForm instmixin add ::myapp::MyWikiForm; next"
4) in the method destroy of ::myapp::Package, do a "::xowiki::MyForm instmixin delete ::myapp::MyWikiForm; next"
There is no duplication of code involved.