This tends to show up if you're trying to tweak/customize preferences (e.g. from the command line or editing plists directly), since you usually have to duplicate the effort for both places.
Even to call it a "system" dialog is misleading, since it's just a system-provided library that each individual app is, technically, free to use or not use.
I certainly agree that it's annoying when the look, feel, and fucntion of all the apps' common interactions don't match each other. I do recall a time, though, when the system library features were so anemic, that I was actually glad of app's departure from the norm if it provided a useful new feature (e.g. "New Folder" button in a "Save" dialog).
I also agree that makes the suggestion of "use a Finder replacement app" not a solution to your real problem.
Maybe I'm suggesting that, to a nerdy-enough audience, you might have to state your real problem as being with "the Finder and all the system provided file-picking dialogs other apps tend to use".
There's nothing really bad about Finder. It's just sort of meh for a tool that one uses all the time.