Many sites rely on the Admin skin behavior, so removing it would not be a good thing. You can always set the admin skin at the site level to be the same as the regular skin so the workaround is pretty simple.

W.r.t. containers, you can always customize your skin pane to force a certain container to be used for that pane. For example, on this site, the left and right columns have one set of containers specified in the pane and the content pane in the middle has a different set. You can do this as follows:

<div id="MyPane" runat="server" containerSrc="[g]DNN-Blue/Text Header - Color Background.ascx" />

You can start the containersrc value with [g] (host container) or [l] (portal container) or omit it in which case it will default to the same type (host or portal) as the skin. With this approach, you can force a container in the content pane for the admin skin, but allow it to fall back to the default for non-admin skin which will address the issue you have raised (right?).

Nik