IIRC, He stopped ruling Spain when he died. Of course, my memory is very vague.
And, of course, I'd lump Austria (the nation) with Germany, in a more wide-sweeping German/Nordic civ. My 2 cents.
The Great Austrian Empire is another matter. It only lasted 500 years. A great feat; but, not Civilization status.
I would like to see a Habsburg leader out-of-the-box in Civilization 4.