I recently tried out (k)ubuntu 9.04 AMD64 installer CD for a test. I connected a second SATA disk to the system as my first disk is already completely used. I started the install-system and performed the usual steps. On partition layout screen, I chose to manually setup my partitions. The setup automatically detected my SWAP partition on the first disk and marked to use it (so far no problem, this doesn't implicate a change to the boot record of course). I reverted this suggestion and made my own layout (including swap) on the desired second disk. So there should be in fact to changes to the first disk - and I'm installing the boot loader (grub) to the second disk's MBR. But: The final screen (before setup begins with the tasks) shows me a summary where the first disk is "changed", too. I wondered and thought I did something wrong. So I went some steps back to verify. Nothing changed. I reproduced this by rebooting and trying again. The summary always shows that it wants to perform changes to the first disk's MBR, too. I was brave (ok, I did a backup of the MBR before) and decided to continue the setup. It seems that it didn't change anything to the first disk's MBR (but I didn't diff it to my backup). Long story short: It's scary for the user if the setup says that it wants to do changes to a disk which it isn't supposed to.
A recent test (ubiquity from Lucid-daily CD) with more or less the similar setup didn't show former described behavior. Installed to 2nd HDD and summary screen only showed planned changes for 2nd HDD's MBR (even though using swap on 1st HDD). Seems to be resolved/fixed.