In the case that a "normal" filesystem is used, such as FAT, it isn't written out to the chips. NAND flash has special requirements about how it is written that prevent a normal FS from being used on it. There is a software layer between the filesystem the operating system sees and the flash chips. The operating system does not directly write to the flash chips unless it is using a flash filesystem. FAT32, ext2, and other non-embedded filesystems are not written directly to the flash.
Here is a company that sells flash chips that can be used with normal filesystems:http://www.m-systems.com/site/en-US/Technologies/T echnology/TrueFFS_Technology.htm
On that diagram the DiskOnChip is the physical device. You can see that there is quite a bit going on between what the operating system "sees" and what actually gets written to the chips.