This is a list of major known issues.
With the current version of the IntuneWin32App (v1.4.2), setting a dependency is not possible. However, the dependend program is uploaded to Intune. The workaround is to set the dependency yourself.
The Error you will get cuase of this is: Publish-IWDWin32App : Error adding dependency for XXX A parameter cannot be found that matches parameter name 'eq'.