No. The format on the flash drives is FAT.
As long as your OS understands how to talk to a USB drive, it'll be able to read it because just about every OS can read and write to FAT. You almost never need to format a flash drive - it comes preformatted as FAT.
FAT32 hard drive partitions are a different beast.
So no, you don't need to worry about how you format your hard drive as far as talking to a USB flash drive is concerned. Linux, XP, Win2k, OS X, WinMe, Win98SE can all talk to USB ports and can read flash drives. You can write to it in OS X and read it in Winders and Linux, and vice versa. The flash drive doesn't care what the native hard drive file system format is.
HTH.
Cheers,
Scott.