Update: Downloading the Windows App should now show "Mattermost" as the publisher if you receive the Windows SmartScreen.
As mentioned previously, we'll also look into upgrading our certificate for a future release, so that the Desktop App will appear trusted by Microsoft, even if only a few people have used the app. This would allow us to bypass the SmartScreen in the future.
Thanks everyone for your feedback across our community channels -- please let us know if you have any further questions!