About NTFS having problems with unaligned start of the partition (start at sector 63), it seem strange to read: http://technet.microsoft.com/en-us/library/cc781134(WS.10).aspx
> Formatting Volumes: Formatting also aligns clusters at the cluster size boundary.
Same for FAT created on the other OS, we can read a bit further:
> Because formatting in Windows Server 2003 aligns FAT data clusters at the cluster size boundary
The FAT filesystem cluster aligment can be modified (and it seems to be the same for NTFS) depending on the alignment of the first sector; it means that you will not generate the same FAT for two partition which have the same size but are aligned differently - as a consequence you cannot directly copy them neither (by "dd").
The Gujin bootloader is aware of that when creating FATs.
I did not find such a field in the EXT2/3/4 filesystem to ignore some sectors at the beginning of the FS.
About bootloaders and 4096 sectors, the Gujin bootloader may be able to help thanks to its minimal IDE driver in the 512 bytes MBR, but the problem is a lack of hardware to test: http://www.wdc.com/en/products/products.asp?driveid=336
says drive WD10EACS has 1,000,204 MB and 1,953,525,168 sectors, i.e. (1,000,204 * 1000 * 1000) / 1,953,525,168 = 512 bytes/sectors http://www.wdc.com/en/products/products.asp?driveid=763
says drive WD10EARS has exactly the same 512 bytes/sectors
and WD10EARS-00Y5B1 doesn't even have a hit on WD web site... Is that available in UK?
BTW, GPT is quite easy to use to define partitions.