The shipyard seems to create a ship with faction protections even though the ship does not have a faction module to secure it.
https://youtu.be/_0BL5OJiYmg
Recommend:
C and v linking behavior for permission modules, c on the permission module and v on the blocks to have altered permissions. This should enable access to the shipyard docked entity/design without having to warp the entity out when completed.
As far as the faction inheritance, faction protections should only be applied to entities having a faction block on them with exceptions for docked entities not using a permissioned(public) dock. The entities that are docked through a non permissioned docking point should inherit faction protection from the mother entity.
If a turret or ship without a faction block on it is blown off a mothership, that entity will lose its faction protections. In the case of ai controlled entities the entity will continue its behavior when it was docked, it just wont have the faction access denial it had previously.
Placing a permission module next to a faction protected entity core, will allow operation of the entity but not build or logic modification, computer weapon/affect linking in the hotbar menu should still be allowed.