Does "Configuration" only control Initial Installation Protection ?

As installed I can choose Configuration Security settings of Internet, Proactive, or Firewall,
and my choice alters the Protection Level Settings for AntiVirus, Firewall, Defense+, and Sandbox.

I can subsequently make manual changes to these Protection Level Settings.
Will Comodo’s protection now be EXACTLY defined by my Protection Level Settings,
or will there be some subtle affect determined by which Configuration Setting this is under.

I was advised 1 or 2 years ago that the Configuration mode had some such subtle effect in Version 3,
and I never could get my head around that.

My specific need at this time is to normally use the default Internet Security configuration until I am comfortable with using Sandbox in the Proactive configuration, and since I will never need Game mode I plan to use change the Firewall Configuration for Maintenance tasks with the Firewall blocked and A.V. and Defense+ disabled.
Last year my Partition Manager lost all partitions even though I had closed all “Applications”.
What I failed to do was disconnect the Internet and switch off Comodo - coincidence ? ! ! !