How to select which thumbnails sizes are displayed in srcset

The 2nd argument of the_post_thumbnail() is an array of attributes and values, so you can just set your own srcset attribute that way:

the_post_thumbnail( 
    'my-custom-size', 
    array(
        'srcset' => wp_get_attachment_image_url( get_post_thumbnail_id(), 'my-other-custom-size' ) . ' 1000w',
    )
);