Those are two different issues.
The periodic tasks are for system maintenance (not disk maintenance), and are performed on a scheduled basis when the system is turned on. The system will check for overdue tasks (the Mac was turned off at that time, for example), and will perform overdue tasks in the background when needed.
IMHO, you should be concerned about extreme fragmentation if you have it. Your OS X system automagically keeps certain areas of the hard drive under control, along wiht a certain file size range, mostly very small files. Modern operating systems are not so much affected by fragmentation, but there are several issues that can make that much more noticeable. Audio recording direct to the hard drive is one. Another is if you let your hard drive get too full. That 15-20% free space is a good rule of thumb to follow on your boot drive. Fragmentation is only one of the issues that might give you problems with a full hard drive.