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',
)
);