I don't know the answer to your main question, but if you want to move or delete Chess, etc., you can do so by opening each program's Properties, unlocking Sharing & Permissions, and setting all named groups to have Read & Write permission. In some cases, it's not possible to move a program even after unlocking permissions, but you should be able to Copy then Paste the program into another folder then move it to Trash. Emptying trash may fail for some system programs, but they can be emptied after rebooting.
For myself, I have no interest in deleting system programs, but I prefer to organize them into subfolders according to my own long-established system. This was a pain in the neck to do under Lion, but eventually was possible in all cases except for a few programs such as RAID Utility, Podcast Capture, etc. that Lion put in the Applications/Utility folder but would not allow me to hide away into a subfolder. But I can live with that.