I believe currently only those who has Bamboo server admin permission could manage agent capabilities/executables.

Some times, the Bamboo admin may want to grant an owner of some build plans the ability to manage the capabilities of build agent. So that the owner of the plan would not request the bamboo admin to add capabilities every time. And at the same time the admin may not want to let the owner has the admin privilege to the whole bamboo system.

It might be good to create a new tick box for the permissions to manage agent capabilities.