I'm not sure, but I think you are confusing two different things:
1) The AF-Area mode, which is set via the AF button on the front of the camera. This determines how many focus points are used for focusing. Since you aren't using Auto-area AF (or, presumably, 3D-tracking AF), you are choosing whether to force the camera to use only the AF point you select (Single-point AF) or to also use points surrounding the AF point you select, either 9, 21, or all 39 points.
2) Number of focus points, set by Custom menu item a6. This is poorly named in the manual. It would be better named number of selectable focus points. All it does, when set to 11 points, is restrict which focus points you can select with the the multi selector.
These two things are independent. That is, if you set a6 to "AF11", you'll only be able to manually set one of the 11 indicated focus points, but if you have one of the Dynamic-area AF modes selected, the camera will still use the surrounding AF points -- including ones you can't select manually -- to dynamically focus.
Note, too, that in a Dynamic-area AF mode, when you first push the shutter button half way, the camera focuses using the focus point you selected. Only if the AF system detects that the subject has moved do the surrounding focus points come into play. So, if you're testing in a situation where neither the camera nor the subject moves (and have a good AF target under the AF point), there isn't any significant difference between Single-point AF and Dynamic-area AF.
In all cases, the info screen shows which AF points may be used by the camera once you press the shutter. In any non-auto AF mode, the one you select is the primary one, and autofocusing starts with that AF point.
Hope that helps, and if I have misinterpreted the question, I apologize.