An MD5 checksum is stored in the .pdb file for each source file. If you answer "No" to the question above "Would you like the debugger to use it anyway?", it prints out the checksum it was looking for:
Using a hex editor, you can see it is definitely in the .pdb. My next task is to figure out how to get access to it programatically. For a .pdb file, I want it to return all source file names and their MD5 checksums.