All of the skins are included by design, so that you can call specific ones at any time, depending on your circumstances. For instance, in one project I have five skins. Each one loads the help with a different pane as the default (Default opens TOC, Index opens Index, etc.). The URL to call each is slightly different, but if the skins weren't included in the output folder then I couldn't call them (the user would get an error).
I couldn't see a way through the GUI to add a conditional tag to a skin. You might be able to manually edit the skin file to add the conditional tag (make a copy of it first). I suggest you put in a feature request, though, asking for the ability to apply conditional tags to skin files. Put in the feature request at
http://www.madcapsoftware.com/bugs/submit.aspx.