I somewhat disagree with your statement. You can use MBR disks as long as you follow these steps as described:
1. Launch "diskmgmt.msc" to auto-detect any new disks that you may have added.
2. Launch "diskpart" in an elevated command prompt window
3. Select the disk you want to partition
4. Then run the following command "create partition primary align=32"
5. Exit diskpart utility and close command prompt
6. In the "diskmgmt.msc" rescan the disks
7. Select the disk that you created the newly aligned partition in step #4
8. Right click on the partition and select format
9. Give the new volume a label
10. Select NTFS
11. For block type, select 4096k.
12. Select quick format
13. Click OK
14. Assign a drive letter i.e. 😧 or other available
If you follow these steps to a tee, your MBR partition will always be aligned even if you import it from a Windows 2003 server. As long as you follow the above steps, nothing says you cannot use MBR partitions in Windows 2003 and then later move them into a Windows 2008 OS.
If on the other hand, you are setting up a clean Windows 2003 Operating System, one way to ensure that you have an aligned OS partition is following these steps:
1. Boot using a WinPE Windows media CDROM
2. Launch diskpart
3. Select the disk you want to partition
4. Then run the following command "create partition primary align=32"
5. Assign a drive letter i.e. C:
6. Exit diskpart utility
7. Perform a quick format using the format command in dos prompt i.e. format C: /q /a 4096 /fs:ntfs
8. Reboot the system
9. Install Windows 2003 on the newly created partition without formatting it in the installer.