alt Hacker NewsThe game installer can't control the layout on an HDD without doing some very questionable things like defragging and moving existing user files around the disk. It probably _could_ but the risk of irrecoverable user data loss or accidentally corrupting a boot partition via a bug would make it completely not worth it.
Even if you pack those, there's no guarantee they don't get fragmented by the filesystem.
CDs are different not because of media, but because of who owns the storage media layout.
It's less about ensuring perfect layout as it is about avoiding almost guaranteed terrible layout. Unless your filesystem is fully fragmented already it won't intentionally shuffle and split big files without a good reason.
Single large file is still more likely to be mostly sequential compared to 10000 tiny files. With large amount of individual files the file system is more likely to opportunistically use the small files for filling previously left holes. Individual files more or less guarantee that you will have to do multiple syscalls per each file and to open and read it, also potentially more amount of indirection and jumping around on the OS side to read the metadata of each individual file. Individual files also increases chance of accidentally introducing random seeks due to mismatch between the order updater writes files, the way file system orders things and the order in which level description files list and reads files.