If your installing as admin, the install procedure does not inject the necessary information into the user's default mail profile, hence the need to run the 'Add to Default Mail Profile' app.
If you want to completely automate the install:
You have 2 options:
Option 1. Temporarily give the user admin rights to the PC and install using the user's credentials. Doing it this way will automatically put the Desktop Msg infomation in the users default mail profile.
Option 2. Create a script that will perform the following:
1. Install Desktop Msgr as Admin user.
2. Inject a RunOnce registry entry on the user's windows profile to 'Add Desktop Messanger to User's Defualt Mail profile' or Just temporarily add the command to a login script for that user.
3. Force reboot
4. Clean itself up
Once the user logs in, the runonce registry entry or the login script will be ran and the user will then have CP Desktop Msgr in their default mail profile.