JoeC's heat die is 120mm^2, as opposed to Bill's 100mm^2.
As we all know, the TIM thermal resistance is proportional to the inverse of the surface area.
The TIM thereby has about 20% lower thermal resistance than Bill's setup, so there's some of the difference.
More of the difference arises in thermal density and its effects on the waterblock. The surface area presented to the block in Bill's test scenario is smaller. Now a smaller die "footprint" equates to a smaller concentration of heat that is presented to the water coming into contact with the wb. This is offset a bit by the spread of heat through the wb base-plate though, but given an assumed fixed value of
h, being the rate of thermal convection, measured as W/m^2K, we are again left with a situation where a smaller die has less effective cooling "effort" acting upon it, resulting in a higher C/W for the block itself (which Bill has coined as T/W), even after discounting the TIM.
Now the thermal density effect is not going to be linear, again highly dependent upon the wb base-plate thickness, but we given the bp thickness that seems apparant on the SlitEdge, one could probably predict a 10-15% higher block T/W.
Weighting out the predicted proportion of TIM C/W and block T/W, we can predict that we're roughly looking at something a bit more than a 15% higher C/W for BillA's test-setup over JoeC's test setup for any particular wb that gets tested, again dependent upon bp thickness. Thicker bp's will incur a less significant relative "cost" for smaller die sizes.
The rest of the differences (~5%) can easily be accounted for by Bill's rationale above.
At least that's my take on the situation. Where it gets confusing for the common reader is when they see Bill's and Joe's C/W data presented on the same page, and people mistakenly assume that JoeC's naturally lower C/W figures means that certain blocks are better than those tested by BillA, as witnessed by someone sparking up
this thread over at OC.com forums.