Good question, maybe this helps : (from Apple)
" You can also verify and repair user permissions on a Mac OS X startup disk. Occasionally the user permissions associated with files or applications become damaged, which can prevent a file or application from opening.
To repair a disk, you may need to log in using an administrator account. If you aren't logged in as an administrator, enter an administrator's name and password when you are prompted. "
Link
Meaning if you are logged in as admin it may not be necesary to close all the apps ... could be