An Alternate Project Manager has every capability on the project that the Project Manager does except that an alternate cannot change the values of the Primary/Alternate managers on the project. The idea behind this is so if the Project Manager is unavailable for some reason or for a period of time, the Alternate can step in and take whichever actions are needed on the project. So it is just a way to say that the designated person is a second project manager.
If a Primary manager value change is needed, and the original Primary is no longer available, an organization administrator will need to step in from Admin and make that adjustment.
Does that make sense? Please let me know if you have further questions.