There are a LARGE number of areas where this is not provided, such as the text color of a disabled control or the checkbox area of a checkbox control. Even for the cases where such customization points were provided, many of them were broken when theming was added in Windows XP and in comctl32.dll version 6 in Vista, which ignores some of them in favor of theme colors or images. Menu colors, for example, are ignored when theming is enabled.
The result is that if you want something approaching a reasonable dark theme with Win32 stock controls, you will often need to resort to full owner-drawing of the controls. This is not a minor task.
Some controls like buttons, list boxes, list views are reasonably well behaved, especially when theming is turned off. Combo boxes and toolbars are more temperamental. Check boxes, scroll bars, menus, and message boxes require a lot of custom painting work.