Was wondering if that was going to bug anyone!
The reason is not so much technical as practical: by managing the location where the game are, I can ensure that everything is always laid out correctly, which simplifies the environment during game run time. Essentially it "normalizes" the layout of the game files regardless of where they originated, be it from a physical disk, disk image, ZIP file, or subdirectory. It also means I can offer a logical "delete" function, where I don't have to worry about potentially deleting something important.
I realize this takes more disk space, but for the games in question, even the sum total is not all that significant these days. If it really bothered you, you could probably open the install folder and change the lec-xxxx folder into a soft link to the directory where you have the files. However, if you do that, stay away from the "Delete Game" option in that case!