Problem
Currently, there's no nice way for other modules to store additional configuration inside the entity display. Although field formatter settings alter will store the information, this is not the right way. Other modules like field group, display suite etc will even need to maintain their own set of configuration.
API Changes
Likely. The idea is to create a new property on the entity display, which is a dumping ground for other modules. It will hold an array which keys are the module and the values are the configuration which the module then itself stores its information in.