While making changes to the security in AX, even though this is done within the client and not in the development environment, it will make changes to objects in your current model and layer effectively making a modification to AX.
This may fill many of us with horror: "I thought we were just ticking boxes in data!" but it has some really great benefits (once we have recovered from the shock of this realization).
One benefit is that we can design our security model and move it easily to User acceptance testing (UAT) and then live. Be completely sure that the security will behave as it did when tested.
The other benefits are that we can draw from the layer technology to extend Microsoft's or our partner's security design ...