Here is what I have done so far:
I set SystemURL to http://nice.short.address.at.my.uni
Site Map -> ACS Kernel Parameters
I set hostname to nice.short.address.at.my.uni in the AOLServer config file (not sure if this was needed though)
After doing this I noticed an interesting behavior-whenever there is a lagging slash in an address ( http://nice.short.address.at.my.uni/dotlrn/ ) the short URL is returned, but an address without it /dotlrn/admin returns the long URL. I am going to revisit this after talking with the guy who set up the Apache proxy (rewrite rule weirdness?).
