If all pages based on the layout are only used in content, you can safely set the property 'Use main placeholder' of the layout to 'No'. This will make the deprecation warning go away. For more information, see the following article:
Use 'Edit/Find Advanced' Search for 'Page open locations'. 'All pages based on layout'. Select the layout and check in the results the column 'location' for 'content' or 'pop-up'. Should be all 'content'