Managed Setup (ManagedProject) has nothing to do with the deployment logic. Managed Setup only controls the integration of the MSI and GUI. Whereas the deployment algorithm is fully controlled by MSI.
If you have two MSIs behaving differently you need to compare them and see what causes the difference. The easiest way to do this is to compare the WXS files that were used to produce MSIs. You will need to set PreserverTemporaryFiles to true in order to collect WXS files.
If you have two MSIs behaving differently you need to compare them and see what causes the difference. The easiest way to do this is to compare the WXS files that were used to produce MSIs. You will need to set PreserverTemporaryFiles to true in order to collect WXS files.