Create a folder named includes in the root of your plugin folder; and place your additional php files inside of there. They (andchild folders and files) should then be copied over with plugin-zip.
If you have a php file with the same name as your plugin in your plugin’s root folder; that will also copy over as well. (e.g. your plugin is named super-rad-explosion; plugin-zip will also copy oversuper-rad-explosion.php in the root folder of the zip).