So why the heck am i getting this error? I set up the permissions the way i want them and it keeps prompting me to "upgrade permissions". However this simply breaks the site for customers.

how do i suppress this message, so other admins dont accidentally click "upgrade permissions" and break things.
As far as i can understand from this article, ( https://confluence.atlassian.com/jirakb/resolving-permission-scheme-errors-838416389.html ) this is the "recommended configuration" if you are using "public" users. I have no such requirement, all my users will be created and administrated accounts from active directory.
If you don't fix this error, then administrators won't be able to add customers to the project, public signup will e disabled, and service desks will be restricted to customers who are added to the project.
well great! thats what i want. don't tell me i am in error stupid website!