It's true, winesetuptk is very usable (It's a wizard), and winecfg look more complicated than anything in windows. I did read that some very simple programs could run without a windows like filesystem. As winecfg is a winelib app, I suppose it may be possible to run it without a windows like filesystem, so wine could look for a registry (Winecfg works with a registry, not a config file), if it doesn't find it, it starts a wizard-like version of winecfg that allowsthe users to get wine ready to run, like winesetuptk does.
The way winesetuptk does it seems less likely to result in mistakes by users.
That's very important for usability and it's why the first time one runs wine he should get a configuration wizard. The "Power user" winecfg (What is currently in the CVS) could be in the wine menu with the wine programs (How this menu is generated, with ros explorer or a specific linux/winelib app isn't really important) with the configuration wizard. This way, users just wanting to change the configuration can start the wizard again, and anybody wanting to tweak the configuration can use the "power user" version