These options affect migration processes:

Display timers when processing
When developing large, complex migration processes (where you are implementing your own hooks), it's important to optimize processing as best you can. To help diagnose performance problems, enable this checkbox to display cumulative timers upon completion of an interactive migration. The migrate module's own hooks use Drupal's timer_start() and timer_stop() functions to track their timing - you can also add these calls to your own hooks.
Cache content set counts
With large amounts of data, particularly when your source views join multiple tables, loading the Dashboard page can become quite slow populating the Rows in set column. Checking this box saves the current row count in the database, and the dashboard will retrieve this value rather than recounting the rows every time. To update the counts, return to the settings page, check the Refresh cached content set counts toggle, and Submit.
Ignore missing advanced help module
Checking this toggle disables messages displayed when the advanced help module is not active. If you're reading this advanced help page, this toggle is irrelevant to you.