How I can change the condition or compare operator for WP_Query in pre_get_posts

You can achieve the OR relation using the tax_query argument like so:

$query->set( 'tax_query', array(
    'relation' => 'OR',
    array(
        'taxonomy' => 'category',
        'terms'    => array( 2, 3 ),
    ),
    array(
        'taxonomy' => 'post_tag',
        'terms'    => array( 10, 13 ),
    ),
) );

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