Yeah I used the same method as you to mark where components are touching except I used some car wheel bearing grease as Its cheap a plentiful. My point was more thinking of a design that "J" proposed that has a plate of copper maybe 2 to 3mm thick with an acrylic top. To mill relief's only 1mm or 2mm deep without going through the plate would be tricky without a stable mill bed. Using protrusions for core ram is the other way that avoids this but then if you are making a one piece block the height difference / chip contact is very difficult to ensure, unless you accept using a chewing gum type Tim. Look forward to seeing your cooler in the "flesh"
MMZ_TimeLord 