All of them may/will be altered.
Take /boot for example. Mine is on a separate partition (hda1) and I have manually created the subdirectories gentoo and clfs for gentoo and clfs specific files. Currently, hda9 is mounted at / when I use Gentoo. Now assume that I want to reinstall Gentoo on hda9. The installation process will create a /boot directory on hda9 with the Gentoo specific files. I would then and copy these Gentoo files from hda9 to /boot/gentoo on hda1. Then I would edit grub.conf and the reinstalled Gentoo's /etc/fstab and viola, my reinstalled Gentoo is sharing the /boot partition with CLFS. In this case only hda9 was overwritten and all the other partitions were left untouched.
Hopefully that makes some sense.
Take an alternate example. Now when I reinstall Gentoo, I tell the installer to use hda9 for / and hda1 for /boot. When the installation is complete both hda1 and hda9 will have been overwritten. I would have lost the CLFS files and would then be unable to boot into CLFS. This would be bad since I use CLFS every day and it would make me cry.
To answer some questions I ignored from your original post...
The MBR and the partition that mount at /boot are not the same thing. If you do not reinstall your bootloader (GRUB, LILO, etc.), your MBR will remain untouched. The advantage of using a separate partition for /boot is that it can be unmounted after the kernel is loaded; your system is more secure and less susceptible to the, "Oooops, did I just delete that?" virus.
Installing GRUB (including using a floppy, CD, or installing to other than hda) --> http://www.gnu.org/software/grub/manual/grub.html
. Read the 'INSTALLATION' section. However, GRUB will boot Windows, so there's no harm installing GRUB on hda.
Yes, /dev/hdb2 is correct for GRUB.
Hopefully that all makes some sense.