Installing Viso 2016 and Project 2016 MSI w/ CTR?

To add to the what's been said already, we went with manoth_msft approach during our Office 365 ProPlus rollout and it worked well. This allowed us to use our Volume Licensing with Click-to-run installing Project/Visio 2016 alongside Office 365 ProPlus Office 2016 version.

Here is an example xml setup for this configuration: 

<Configuration>
    <Add OfficeClientEdition="32" Channel="Deferred">
        <Product ID="O365ProPlusRetail">
            <Language ID="en-us"/>
        </Product>
        <Product ID="VisioProXVolume">
            <Language ID="en-us"/>
        </Product>
        <Product ID="ProjectProXVolume">
            <Language ID="en-us"/>
        </Product>
    </Add>
    <Display Level="None" AcceptEULA="TRUE"/>
</Configuration>

Having to use a MAK setup wasn't ideal at first, having to meet the minimum amount of units but it worked fine in the end.

Hi Eric, technically it is not supported to run an MSI and a C2R-based product from the same release (e.g. Office ProPlus (2016) C2R and Visio 2016 MSI) on the same box. But if your using a KMS server or ADBA for activating Visio/Project and you have a volume-license agreement in place, you can opt to run the C2R-based volume license releases of Visio/Project: https://technet.microsoft.com/en-us/library/mt703272.aspx

This enables you to run two different license flavors (volume-licensed Visio/Project and subscription-based Office) with one deployment technology (C2R) on the same box.

There was an offer to get a matching C2R version, but it expired afaik. The "upgrade offer" page now redirects here: https://support.office.com/en-us/article/Error-Stop-you-should-wait-to-install-Office-2016-We-ll-have-to-remove-the-following-if-you-continue-a225347f-e102-4ea6-9796-5d1ac5220c3b?ui=en-US&rs=en-US&ad=US

They did relax the requirements, the latest supportability matrix is here: https://technet.microsoft.com/en-us/library/mt712177(v=office.16).aspx