The first link is saying that
- If the drive was formatted FAT32 before Windows XP (or maybe 2000)
- the clusters on the drive will (or may?) not be aligned on 4KB boundaries
- which is what NTFS actually wants
- and then the CONVERT utility will then create 512-byte clusters
- which are less efficient
So it suggests that you run a utility to make sure the clusters are aligned before you CONVERT.
The issue with new 4KB-sector drives is different. If you have 4KB clusters (which is likely) then if they are not aligned, that's bad in terms of I/O because you have to do two reads/writes for each cluster. But this earlier problem is that it won't CONVERT to 4KB clusters, which is bad for I/O because you have to do more reading/writing of smaller clusters.
The problem described at the first link is (1) not an issue only with newer AF drives; (2) is an issue converting from FAT32 with any drive; (3) might be fixed in Windows 7 if the CONVERT is smarter and more aggressive -- fixing the alignment requires more work.
If you can verify that the FAT32 clusters are already aligned, then it won't be an issue. But no easy, non-geek way of doing this with Windows comes immediately to mind....