I have not tried this in VMware Fusion 5 however I'm presenting this as informational and you can try it to see if it has any affect.
In VMware Fusion 2.x when selecting "Never" vs. the default "In Unity" for "Show running virtual machine applications in the Dock" it added the following option to the Virtual Machine's .vmx configuration file.
proxyApps.runGuestProxyApps.unity = "FALSE"
By default the value for that option is true and is not present in the .vmx configuration file until the default is changed or added manually. So if the option is present it would toggle FALSE/TRUE as appropriately selected.
Have a look at: Editing the .vmx file for your Fusion virtual machine (1014782)