It looks like GBNG cannot be disabled in PageOrder.
In some quick research this looks like a side-effect from SAK-27912 in Sakai 11 making tools that "allowDisable" a little more specific and doesn't allow tools without a functions.require to be disabled. It also doesn't allow tools with site.upd or site.visit as a functions.require to be disabled.
I don't know why site.visit is excluded from the allowed permissions. I think to fix this we'll either have to.
1) Modify SitePageEditHandler to allow site.visit in functions required and add this to Gradebook NG
2) Add a new shared permission (gradebook.read?) and backfill that to all users since nothing is shared between all roles currently for gradebook and I don't see anything else that's shared.
It looks like this is for any tools that don't have a specific functions.require, so it's not just gradebook. Fixing this might involve adding new specific "read" permissions for every tool as a functions.require.