Seems like remote source chilled water would be treated like purchased
heat under G3.1.1.1, where you would come up with an equivalent cost
rate based on how the remote central chiller plant is purchasing energy
and all other efficiencies related to producing chilled water and
pumping to your building. Then you would have to use that rate in both
baseline and proposed buildings, similar to an electric or gas rate.
This is just my guess, anyone else have an idea from Bldg-Sim mailing
list?

So to answer your original question in HAP, you would choose remote
source chilled water, the same as proposed building, with same cost
rate, then change all baseline cooling to chilled water under each of
your systems. This will essentially make chiller water "cost neutral"
and not give you an opportunity to improve in cooling efficiency over
the baseline building.

I came across this document which may be helpful as well
http://www.usgbc.org/ShowFile.aspx?DocumentID=4176.

Tyler Whately, E.I.T.