Accesses don't wear flash significantly compared to writes. Heavily read pages of NAND flash do need to be rewritten occasionally, but I can't imagine this alone would ever cause a device to reach its wear limit in normal use. NTFS does write more than FAT32, so you're still correct that FAT is better for reducing wear. FAT's fault tolerance is notoriously bad though.... would you rather lose your data or have to replace a $20 usb stick (which will probably be $2 by the time you wear it out)
Flash drives have a flash translation layer that makes the flash look like a regular disk despite having special properties. This layer handles the wear-leveling, garbage collection, and bad block detection so the standard filesystem (that was designed for magnetic disks, probably) doesn't have to consider them. Regardless of the filesystem used, the wear of the device should be related to the total amount of data written, not the location of the data.
The solution of this problem is trivial and is left as an exercise for the reader.