1. This only changes the BIOS that is loaded to RAM. No info is stored to MB, all the changes are made during the win boot (that's why wcprset is needed). But still, that HEX code contains all the info all HW (CPU, RAM, everything...) is controlled, so you can easily burn your RAM. Some people rewrite memory controling sofware here.
2. The IDE is not disconnected in bios, just it's ID is changed. And yes windows don't use the BIOS to excess the IDE, but SF does. And the non-working ID doesn't allow SF to acces that IDE directly.
3. The IDs: the first squere on the top is the device ID rewriten from the second red squere. The lowest red squere is the ID which SF (and other non-win) software uses.
4. If you want to know everything read the original review