A bit of Googling indicates that it's to allow the OS to install the Adobe "Speed Launcher" - is this it or are there other components that are more tightly into the OS that it must have to have closed so that it can update them?
It was all working before I had to scrub, so I know it's possible to get 64 bit and 32 bit to play nicely together.
The main reason Reader is going to need a reboot after updating is because the Active X component and Explorer Shell Extension have been updated.
Since these items are almost certainly being held open by Explorer (remember, also hosts the desktop) or Internet Explorer, they can't be updated while either of those programs are running.
The replacement of the actual file is scheduled for reboot, and you get prompted that it needs done.
The alternative is to make sure that all instances of Explorer and IE are shut down (for all logged-in users) before running the installer.