Most enterprise organizations use Visio and Project along with their Office 365 installations. The problem they run into is the MSI compatability with Click2Run installs of Office 365. Until mid last year the Click2Run for Project and Visio did not exist but since than the Click2Run installer has been made available from Microsoft.
Shown below is the compatability chart for users with specific versions of Office 365 and 2016 and what the install experience would be if they went with the Click2Run vs MSI installer. This will assist in stratergizing the combination of the deployment.