The formatter aught to correctly align the partitions, and leave space at either end. Some cards were known for using exposed logical blocks at either end for internal crap, and wanting very specific alignment, that would perfectly match a FAT32 file system. If they didn't get it, they could run slowly, due to lack of alignment, and/or bug out if your data was in the way of expected scratch space, or space for encryption info, or whatever else.
TMK, all the Panasonic SD Formatter does is write the partitions and main FAT table at erase block aligned boundaries. I can't say that's 100% of what it does, but AFAIK, that's basically what it does. Allegedly, the standard calls for 4MB alignment, and many cards use 4MB erasure blocks, but performance tests seem to make it look like there's everything from 512K to 8MB blocks out there, so...?
Since my recent SD cards have not been compatible with the Panasonic SD Formatter (Samsung, Kingston, Patriot), what I've done, just in case, is make images of them, while blank, with dd, then keep a compressed image in case I need to format one in the future (a sparse write of an image that's mostly zeros should be OK on the flash).
My last Samsung 32GB class 10 uSDHC consistently gives >18MB/s sequential read, about 4MB/s 4K random read, and ~11MB/s sequential write (as per CDM); yet is partitioned just like a regular hard drive would have been, down to the partition beginning at sector 63. So, even with all the alignment bits said, there are definitely exceptions.
The SD specification not being fully open is kind of annoying, when it comes to this stuff, and that SD controller makers didn't have to things anywhere near right
, like CF.
P.S. Nice article on the issue: http://www.olpcnews.com/forum/index.php?topic=4993.0