Fix #1595: Set ptl_multi_layer_enabled_flag when more than one layer is encoded
This solution sets ptl_multi_layer_enabled_flag automatically, when more than one layer is encoded.
This reduces the usefulness of the MultiLayerEnabledFlag command line parameter to the case, where enabling the flag for a single layer is wanted.
An alternative solution would be to fail instead of a warning and ask the user to manually enable MultiLayerEnabledFlag.