How do we manage 365 upgrade of different combo's of existing Office 2016 (MSI) installs?

Everyone of our end users has Office 2016 (MSI).  We have a mix of end users that also have Project 2016, Visio 2016 STD, or Visio 2016 PRO (all MSI installs).  We just came to the realization today that we can NOT upgrade Office 2016 (MSI) to 365 (C2R) unless we remove all *2016 (MSI) installs.

[We have MECM CB - 2006]

So do I have to make separate target collections for each permutation (Office+Proj, Office+VisioSTD, Office+VisioPRO, Office+Proj+VisSTD, Office+Proj+VisPRO...) and create separate C2R MECM applications for them?

Is there any chance the application MECM creates for me can do intelligent upgrades (upgrading only what's currently installed without adding anything new)?

My initial test shows that anything I list in the xml file for the C2R installer gets installed.  I've yet to find an option to add to the xml file that "installs only if existing version found". 

Please tell me there's a better option than creating separate collections for each permutation of software combo's!