Yeah, that's probably sensible. I just think that, since my app will only have one window, having it listed twice in the Windows menu will look a bit silly. Not that anyone ever looks in the Windows menu...
... and it's a good thing they don't, because the inconsistency between apps is shocking. The one-window apps that Apple ships with the OS all seem to display only one item for the main window, but some of them put it above "Bring All to Front" and others put it below, none of them bother with the diamond mark when the window is minimized, and many of them don't even display the tick when the window is active. Except for iTunes, which displays both tick and diamond, but unlike the other apps hides/unhides the window when you select it from the menu. What a mess!