I'd vote for additional feature in nupgrade script - backing up partition table. Or people should at least backup it by hand
When one screws up something or want to go back, it may be handy for restoring (Or use panasonic SD formatter).

Point is that it looks like both partition table and FAT layout is tuned to be aligned with physical flash blocks. By creating random partition table, speed (and maybe even reliability and durability) may go down.

See this article for details
http://www.hjreggel.net/cardspeed/cs_calign.html

So maybe, if nupgrade.sh does the partition layout, it would be nice if it left at least the beginning of first FAT partition alone.

It is hard to know how important it is, maybe not much. YMMV

When I got my 8GB SDHC card I found that first 4MB of the card is 'wasted' and partition begins on block 8192. This is confirmed in the document mentioned above. There is perhaps some reason for this. I think this may be related to erase blocks and grouping of blocks for internal wear level logic. Maybe they try to prevent wearing off the beginning of the card (as it may contain some critical low level data).
Thisis a bit of black magic. If you are interested, start reading from page 66 of http://www.sdcard.org/about/memory_c...Layer_Spec.pdf
Looks like the size of Allocation Unit (AU) is 4MB for big cards. so it may make sense to aling beginning of partition at 4MB and data blocks after FAT table at 8MB.