Override base Gutenberg block default spacing in child theme’s theme.json

Use a Global Styles Filter to override the style:

add_filter( 'wp_theme_json_data_default', function ( $theme_json ){
    $new_data = array(
        'version'  => 2,
        'styles' => [
            'blocks' => [
                'core/embed' => [
                    'spacing' => [
                        'margin' => [
                            'top' => '2rem'
                        ]
                    ]
                ]
            ]
        ]
    );

    return $theme_json->update_with( $new_data );
});

An alternative that may also work is using the Global Styles UI in the (Site) Editor to change the default style of the block. Yet I think that’s not a viable option if you want your override to be part of a version-controlled theme.