Rick,
I'm thinking about recoloring the skin but not for the orange and black site - I found a free greyscale skin called "Greytness" (?!) at Snowcovered, from Adammer LLC,
which is pretty good, and the client likes the look. But I have another site where the logo is in a medium purple and shades of lavender, and the color scheme of Minimal Extropy simply Will Not Do for that.
I thought the open source license let you play with whatever you like, as long as you don't try to sell it. I'll keep your suggestion in mind of a custom skin with its own name, you're perfectly right about upgrades. I actually like the general look of Minimal Extropy, but the colors are really restrictive. Or, I may use Greytness for the purple site too - it has a much broader arrangement of internal panes than M. E. and I think a greyscale skin would work there.
I don't use Firebug but I have the Web Developer toolbar in FireFox, and it led me straight to a DIV called .logo_pad with a height of 100 px, in the skin.css - I changed it to my needed height (override in the portal.css, just for experiment sake) and voila!