We recommend that each project have a dedicated version of Simulink. All engineers working on that project should work on that project's models in that version. If that project would like to upgrade, it should do so in a single all-or-nothing step.
Here is a helpful analogy. Let us say that you are designing a bridge. Some of your engineers are working in the Metric System and others are working in the Imperial System. Some engineers are comfortable with the metric system and others are comfortable with the Imperial System, so you allow them to use the system which they prefer and they work faster as a result. Soon, you as the project manager, run into challenges interfacing the components of the bridge because each uses a different System of Measurement. You try to use all of the components in the same model without making any changes for the different systems of measurements. When you go to build the bridge, the span is 100m too short and half of the components do not fit together once on site. The project is a complete disaster and costs twice its initial estimate.
The solution to this hypothetical disaster is to enforce a single system of units on all components for the full system, performing the necessary conversion steps when they are needed. Going back to the pain point you are facing, this means enforcing a single version of Simulink for all models in each project. Then Model Upgrade Advisor will help you whenever you want to upgrade.
It would be beneficial for you to ensure that each project for which you are responsible has one version of Simulink. You can pick a different version for each project, but each project needs its own version. Your engineers will then use the appropriate version for each project. If an engineer is working on a project in R2013b and a different project in R2017a, he ought to have access to both Simulink versions in order to work most effectively on each project. He does not necessarily need to have access to both at the same time.
