I'm having exactly the same issue you're having. In our standard we do have a doulbe Allow NTFS permissions entry and this sort of "bug" is not allowing me to set permissions they way I want to and need to do it through Windows instead, making it 10 times slower.. Did you sort it by any chance?
Considering Microsoft are no longer developing Windows PowerShell and are putting all future development efforts into PowerShell Core, I think the question of whether or not the NetApp PowerShell Toolkit needs to be refreshed to work with PowerShell Core is self evident, and the customer want for it doesn't need to be 'tracked'.
It's better to get started now, rather than trying to work with the angry hords banging at the door.
I'm looking forward to being able to begin migrating my lab build code which uses Windows, VMware and NetApp PowerShell modules to PowerShell Core in the future. The NetApp Toolkit is now the last piece of the puzzle.