Ok, I misread Bouwes post I guess...
-If you are setting the skins my previous solution should work fine (installed as host skins)
-Create one skin without / with neurtral the CSS and upload as Host skin.
Create a container for every portal and include the css for the skin in there and upload these per portal.
Now if you pick the container the skin will change too...
(Feels like a Hack, but it does work...)
-I didn't try but I think you should be able to use an include file which is below the portal folder
<!--#include file="../../myinclude.inc"-->
-You could use virtual directories.
-Or you could put the HTML in a usercontrol and load that in the skins