Sysprep removes drivers, but the AHCI/IDE issue is something that window ONLY installs if you are AHCI to start with, i.e. it see's the AHCI and installs the required support files. Not so sure Sysprep covers the Bios change to AHCI.
If you have an OS with IDE, and then switch to AHCI (Newer), then the machine BSOD on boot.