Reason SD cards come FAT formated instead of Fat32? I found my SD card to be FAT formated instead of a modern filesystem (at least fat32).

This comes with the disadvantage of large allocation unit size (32kb) whilst most of the files are less than that.

Is there a reason behind that and can I safely format sd cards to be fat32 in order to use another allocation size (8kb or less) ?

Phone: Xperia Neo V
Generally FAT is used when possible simply because it's compatible with more (older) devices.  While this is not much of an issue today, it probably continues out of (1) very slight market advantage and (2) the fact that factory machinery is set up that way and it would cost owners to change it.

In any event, Android can certainly read FAT32; if it couldn't nobody would be able to use SD cards larger than 2GB.  There should be no problem with Android being able to read your card after a format.