AFAIK - Apple doesn't publish to the general public exactly what happens when "Choose Startup Disk" is used. It's at the core of security and I imagine that is the reason it's not generally available.
I know that "Choose Startup Disk" alters the MBR because it's a protected MBR before I use it and it's a hybrid MBR - according to gdisk - after I use it. If I choose Windows or OS X from the EFI boot screen, the disk remains unaltered with the correct protected MBR.
If you've found Rod Smith's various pages, you've found the same info that I have. It took a LOT of re-reading and cross referencing to get a handle on it. I couldn't even boot from a Ubuntu Linux Live USB when I started. Now I know very well how to create multiple flavors of portable OS's.
I know nothing about Boot Champ except that it exists, first because I don't have a hackintosh and second because I do all of this so that I know how to fix my stuff when I - inevitably - break it. Both Boot Champ and ReFind were possible choices. ReFind's shortcoming is that it presumes one physical startup disk with logical partitions. I found that it gets confused with 4-6 physical hard drives connected.
The EFI boot screen is the "best" way I have found, but I'd love to find another solution so I don't have to keep installing and removing the GT 120 when I want to switch OS's