From the original report (http://www.demographia.com/dhi.pdf http://www.demographia.com/dhi.pdf), it appears that they do actually compare medians as you sugges

From the original report (http://www.demographia.com/dhi.pdf http://www.demographia.com/dhi.pdf), it appears that they do actually compare medians as you suggest: "The Demographia International Housing Affordability Survey uses the 'Median Multiple' (median house price divided by gross annual median household income) to assess housing affordability" (p. 7).