There is no particular issue with using cluster aligned partitions on XP/2003, with the only VERY NOTABLE exception of this one http://reboot.pro/9897/
What is highly debatable is the actual performance difference, which is actually "next to none" impossible to notice without benchmarking and very rarely affecting "anything" substantially in real life usage.
The difference is actually noticeable only on very slow devices (please read as "USB sticks") which more often than not are FAT32 formatted and thus the "new" partitioning scheme is usually INeffective
(and some more "advanced" tricks should be used), see:http://www.msfn.org/...n-its-clusters/http://reboot.pro/16775/http://reboot.pro/16783/
What you are seemingly missing is that there is NO ISSUE whatsoever (exception made for the metioned one) in operating (pre-partitioned, externally or under other OS) disk drives following one or the other convention, and as said an actual speed difference is - at the most and possibly excluding particular Server scenarios - "marginal".
The drivers used by all NT systems (starting from 2K at least) simply ignore any and all CHS data and exclusively use LBA to access a device, the only issue may happen (and it is easily fixable) when booting, because of the CODE in the NT bootsector (both the bootsecto for FAT32 and NTFS is affected).
Right now you seem like attempting to solve a "non-problem"...
Current drives are most (if not all) of the Advanced format type, and there is no actual reason why a filesystem would not work on a non-512 byte sectors.
The issue may come with "particular" apps, mainly - but not only - those that use "direct disk access" (IF they are "badly" coded).
may help you in clearing the ideas