well, i'm not aware that netscape will open a konqueror browser, at least not without hacking the source quite a bit. it doesn't sound like something anyone would program it to do. i can't see where it would ever be necessary or helpful to do so.
for the plugin, it needs to be platform-independant for it to work under both o/s's. if you're using any libraries under windows that aren't available under linux, the program isn't going to compile or work.