Martin from Frontline Education has given us the feedback regarding assigning custom permission sets.

Here is what customer wrote:

Thanks for checking.  I've gotten past it so no confusion but happy to provide some feedback to help for others when this situation comes up next.  It seems Gainsight works differently then the dozens of other packages we have in Salesforce.  In general, these permission sets are additive - meaning if you have a lower level AND a higher level, it counts as the higher level and you get that access.  It is also suggested by others (and a former CSM of ours) to clone package sets so they can be extended with non package permissions to make admin life easier.

So in Gainsight's case.

• The cloned GS Viewer which had extra permissions not related to GS (like editing fields on an account) counted as full even though it didn't grant any actual abilities to do anything in Gainsight.
  • If I also applied the standard GS viewer on top of that custom one - it all of a sudden counted as a View Seat but they retained the extra permissions from the other set.
• If someone has GS Standard and GS Viewer, they still count as full but only have the permissions of viewer.

Again I cleaned things up and am good but the above behavior is odd compared to the rest of the SFDC ecosphere.  It removes a lot of efficiencies as an admin. 

Also,  If someone has manage package license and ZERO permission sets - they count as full even though they have literally zero access.  I would think this would count as viewer.

Has this been reported already or is Martin missing anything here?