Optimizing Linux with cheap flash drives

Note that for FAT filesystems, the start of the partition has very few relation with the data block alignement, because the FAT itself is located at the beginning and is of variable size (depends on the number of clusters).
When I have written the FAT creation support for the Gujin bootloader, I did try to adjust and display the alignment of data clusters, there is all fields needed in the FAT superblock to leave gaps to align anything you want.
Obvioulsy you should not try to *move* the whole partition and change the alignment of the first sector, even if there are tools to do so.