Hello! I have already complimented you on the very nice plugin! I really enjoy it.
Here is my suggestion.
I am building an Intranet, and before using URE, I was using UAM (User access manager) and they had a very nice feature.
If the page was on the mega menu, once the page access is disabled for a certain role ( inside the page edit page) it would automatically hide it in the menu. That makes keeping consistency of access across the site much easier.