The time based permissions you added are incredibly helpful for the image I have for my server however is it possible to add a similar system for the amount of times a permissions-based command is allowed to be used. For example, allowing players to use /randomtp say only 5 times per day, This would readily apply itself to various needs of prison, games or faction based servers in addition to making donor perks easier to control.

That is not the job of the permissions plugin. This should either be managed by the plugin the command stems from or a specialized plugin.

Also it’s not possible to reliably implement this. As a command permission can be checked without the command being executed!

^ pretty much sums up my opinion. I hope you understand why it's not reasonable for me to implement such a feature :)