>> I believe what it *actually* does is yell "hey, somebody changed this!"
>
>  How does it do that? The bios cannot have sufficient info about the
> graphics card in order to show a message on screen, especially if the
> graphics card is currently in non-vga mode.

I would imagine it goes something like this:

Interrupt 13 handler (file I/O) code inside BIOS:

Check if trying to write to MBR (always on the same place)
If not, write as usual to the drive, return
Change screen mode to 720x480 (or whatever that one is the BIOS uses at 
startup) using an interrupt 10 call
Display some text on the sceeen using the same routines as the BIOS setup 
screen etc
Wait for keyboard input (note this totally hangs the system)
If user agrees, write the data as normal to the disc
If not, just exit the interrupt handler

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