This would be a plugin that allowed ops to select regions with WorldEdit, and then apply certain permissions to different groups in that selected area. Example: Say there is a parkour map in a server. Donors on that server recieve /fly, but they shouldnt use it in the parkour map. So with PermRegion, you could select the parkour map area and disallow the essentials.fly (or whatever it is!) for the group "Donor" in that area.
MCMastery a better solution in my opinion is to ask for certain custom world guard flags for example that disables flying in a certain area Because I will do a counter example to your example If a player does /fly outside the region and then walks into the region that the perm is disabled in they could still fly they just can't goggle the command
Thx for the advice! I have also seen a server that toggles /fly to off as you walk into the parkour. tahg (lol)