Can't figure out a way to remove all default minecraft commands (/plugins, /kill, etc.) Yes I know NCP and even Essentials gives a way to remove them yet when I add them to the deny list they still run regardless.

You can remove the permissions for them. (Just debug with luckperms what permissions are checked while executing the commands)

To completly remove the commands you would need a plugin that does that for you.
Wouldn't be of much use though in my opinion.

You can set LuckPerms to use explicit permissions with this config option. This means that ONLY permissions you apply in LuckPerms will be used.

https://github.com/lucko/LuckPerms/wiki/Configuration#apply-bukkit-default-permissions

In addition to what's been suggested above:

/lp group default permission set minecraft.* false will negate all permissions starting with minecraft.