hmm. i dont have a system updates option with the "tasty bread" 2.3.2 im running... let me load up my stock rom and ill get back to you.
edit:
ok,so i loaded up my rooted stock rom and checked for system updates. the update downloaded,verified,and asked if i wanted to install. i tapped install now.
it did some things,rebooted,skateboarding androids,then amon recovery. i chose reboot system,and it continued rebooting. when it was finished i checked about phone again... the update does not appear to have changed anything. i have the same radio i had before,not the one your PDF file listed( 2.42.02.10.29 instead of 2.42.01.04.27) and my rom number is 2.37.605.4,not 2.41.605.6. however,when i check for updates again,it says "your system is up to date". so i dont know if it really did anything or not.
i am,however, still rooted after the update. the superuser ninja is still there,and i still have my "trackball not required" amon_ra recovery. i hadnt downloaded any root user apps on this rom,so i downloaded drocap and took a screen shot just to make sure it worked. it installed and asked for superuser permissions when i ran it.
id say you are fine to go ahead and install the update,assuming you have completed all the steps to rooting(got amon_ra installed,made a just in case backup).