Using the command library Commodore (https://github.com/lucko/commodore) to add command tab completions for Brigadier results in non-vanilla commands showing up in vanilla /minecraft:help, and they will show up regardless of player's having permission to them (vanilla commands in this list do respect bukkit permissions, however).

It might be best to not include non-vanilla commands in this list, since it's not really suitable for showing large numbers of commands, but it really should at-least respect permissions as it does for vanilla commands.