If you make changes to the gaze interaction's dwell time or activation method within the Gaze Interaction Settings, then open Communicator or Compass, the settings in Gaze Interaction Settings may change. This is by design.
Profiles in Communicator and Compass store certain settings such as dwell time. This has a number of uses such as making it easier for users to customize their experience for certain environments (e.g. indoors and outdoors, glasses and no glasses) by having multiple profiles. The whole idea with these softwares is that they provide the user with everything s/he needs. Users are provided a simple and fast way to change the settings that are relevant.
The Method settings in Gaze Interaction Settings (such as dwell time) should be used for products that do not provide those settings internally, such as Windows Control.
The main priority will always be to the users and their ease of access.