Huh?
Can you describe this in better detail?
The boot order is determined by the BIOS, not Windows. When you first turn your computer on, the processor loads the BIOS. The BIOS runs some code that searches programmed devices for a MBR (aka. 'boot sector' and 'boot record'). Once it identifies bootable media, it then boots to the best possible device. This device is generally whatever you select in the CMOS configuration. So it doesn't matter what Windows writes where, it will always boot to whatever device the BIOS specifies... So you can't be talking about this.
What OS information? After the bootstrapping process, the only code really involved in booting are C:\NTLDR and C:\boot.ini. Does it alter these files?
In a nuthshell, once control is passed from the BIOS to the drive/s MBR, the MBR instructs the the processor to run a 'boot loader'. It is at
this point when Windows can finally have control of the boot process. This is where things would
have to go awry, but I don't see how?
Take Windows XP for example - the boot loader is C:\NTLDR. NTLDR instructs the processor to boot Windows or display a menu which consists of a list of installed OSes or other programs. This boot process and boot list is compiled from C:\boot.ini. NTLDR instructs Windows to boot and that's the end of the boot process for all intents and purposes. I don't see how Windows has much room for error here unless it edits the boot.ini? Maybe it damages the NTLDR? These things would happen regardless of your drive configuration though, if that's the case. :\
Excuse my skepticism, but I've been running IDE / SATA together for years and I've worked on many, many, many systems with a 'hybrid' setup. I've yet to encounter an issue like the one you're talking about.
Fortunately, if anything
does happen to the MBR, NTLDR or BOOT.INI, it is a quick snap to repair using the Windows install CD and recovery console. Just one or two commands and you're back in business.
I don't see this as such a huge concern.