Just in case someone else encounters this problem:
Keep in mind this is probably only useful for fellow IT gurus running shared environments.
I have a small lab of PCs with Office 2016 installed (msi, not C2R). The lab is mainly used by students and so the usual restrictions are applied (by GPO). When I initially installed it, I tested with an admin account and with accounts that are already on the PC and all was well.

I’ve since done my usual routine of cleaning off the user profiles and low and behold the non-admin accounts I tested no longer work correctly: I’m getting a message for every new user that logs in saying ‘Word 2016 is not your default program, do you want to set them?’. Obviously this isn’t an issue if we’re only having one user on the computer, but this is a lab so it will have many users and I really don’t want them to come to me every time asking if they should answer yes or no.

The solution: Deploy a registry key (via GPO) which will tell the offending Office Apps to not display the message.

Here’s the process I used:

  1. Create a group policy object which will apply to the users we need to (not computers unfortuately it’s per-user).
  2. Edit User Configuration under Preferences -> Windows Settings -> Registry
  3. Add a new registry item
  4. Use the Update action and set the Hive: HKEY_CURRENT_USER
  5. For Word, set the Key Path to SOFTWARE\Microsoft\Office\16.0\Word\Options
    For Excel, set the Key Path to SOFTWARE\Microsoft\Office\16.0\Excel\Options
    For PowerPoint, set the Key Path to SOFTWARE\Microsoft\Office\16.0\PowerPoint\Options
  6. Change Value name to AlertIfNotDefault
  7. Set the Value type to REG_DWORD
  8. Put 0 in the Value data
  9. Now make sure that this policy will apply to your users and you should be good to go! It might also be a good idea to go into the Common tab up the top and set it to Apply once and do not reapply just for performance sake.

I hope that helps someone out there, I presume it will work on other versions as well? No idea.