Your first point is a good one, and is a good reason to favour LinkFS-style links (which operate via an image filing system) rather than the Obey-file veneers you find in Resources:$.Apps.
As for directly patching !Boot and !Run files, you would have to copy the application to one of your working directories anyway (otherwise the package manager would overwrite any changes at the next upgrade).
One enhancement I had been considering, and in view of this discussion would probably be a very good idea, is to allow any path to be mapped - not just the top level of each hierarchy. In principle you could use this feature to achieve any disc layout.
(In practice, if you want that level of control then package management probably won't be a win for you. I'm not looking to convert everyone - just provide an option that doesn't currently exist.)