Hi,
I am not sure if your issue is resolved since it is in 2015. We have also implemented Fiori and if I am correct, Fiori gets the roles and then call the ARM in GRC.
That in turn should trigger the ARM configuration and etc.
Since you are maintaining a separate custom table for managers, then I think you need to an enhancement in the Webdynpro for the Manager ID field.
Your developer should be able to figure out the place to do the enhancement and SAP does provide an avenue for it -> SE80.
To figure out the place for the logic, in the ARM page, click to the User Details tab. Then right click somewhere near the manager ID field and usually a pop up screen shows the details for the webdynpro. Your developer can then check for the class and method, do some debugging and then from there, they can put some custom code. Hope this helps.