Um...you have me lost on this one! There are no plugins that the dfx installer installs to the skin dir, it installs them to the "default" location aka the Road Runner directory. I would also assume that in the case of the dfx skin, john has it set to not uninstall or over-install any previous exsisting plugins in the rr dir. I think I can count the number of times on one hand that I have used the dfx installers so I unfortunity can't say for a 100% whether its a fact or not, so I'll just go with 99% sure..:).
I know I lost the battle on the "C:\Program Files\Road Runner\Plugins" as default directory for plugins, but for those of us that do use it, it can't be too difficult to check that directory for a specific plugin subdirectory and if exist point the skin installer to it instead of installing another copy in the skin directory. Automated Installers registering plugins is a terrible idea! For example, if DFX4 added all the plugins it's capable of using under its skin folder and registered them -they work great for DFX, but when I'm done looking and delete the DFX directory from my skins directory, every other program/skin that used those registered plugins are suddenly going to stop working, and I don't know why!