It'd be nice if one could save a .aprx file withOUT a default toolbox and/or geodatabase. I see good reason for this depending on the industry and project that you are working within but in many cases, it's simply added fluff. Per the following link, one cannot remove/disable the default toolbox or geodatabse: http://pro.arcgis.com/en/pro-app/help/projects/change-a-project-s-settings.htm . My vote and I am sure many others' would be to have a checkbox to NOT include a default project toolbox and one to NOT include a default project geodatabase. Similar to how you can opt to NOT create a new project folder.