When an engine mapping is performed, is the automatic gear box software also modified?

Yes and no. The automatic gear boxes are actually handled by a separate ECU different from the engine ECU. But the modification of certain engine ECU parameters do affect the way the gearbox will behave and will actually be a much sportier and appealing ride. If you do want to go much further, it is possible to change the specific gearbox ECU software, but with additional costs. It is an operation that is rarely justified.