As I understand the scenario is that the customer does not have an extra SQL Server instance. On order to create a temporary one, they are installing on the SharePoint front-end server.
There is no cause for worry. SMSQL by itself cannot detect the SharePoint backend databases since in this case, it is not being installed on the backend SQL Server host of the SharePoint farm. However, even if it did, SMSQL does not do anything to databases in any way unless you initiate the operation from the GUI.