After spending time debugging export.php, I found that we have to register post_format taxonomy for our custom post type.
register_taxonomy( 'post_format', 'portfolio', array(
'public' => true,
'hierarchical' => false,
'labels' => array(
'name' => _x( 'Format', 'post format' ),
'singular_name' => _x( 'Format', 'post format' ),
),
'query_var' => true,
'rewrite' => $rewrite['post_format'],
'show_ui' => false,
'_builtin' => true,
'show_in_nav_menus' => current_theme_supports( 'post-formats' ),
) );
Easy as that!
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