Hopefully this helps someone, but, the only way I managed to get the client to install silently via group policy as an MSI was to make the following changes and add them as an MST.

In "Feature" table, set the "Level" to 0 for all the properties you don't want - we only wanted ClientBilling, CostPreview, Messaging Client and Print Rules and the Common features (this will need to be there for everything).

In "Property" table you can add the other properties if they are relevant (ARPNOMODIFY etc) and the address of the accounting server

Equitrac 4: EQCASNAME
Equitrac 5: CASNAME

That should be everything that needs to be done and that works for installation and uninstallation via Group Policy for us.