search by meta field in the regular WordPress admin panel search

For regular admin panel search you should include “is_admin()” to be true.
For checking for specific post type you should check from $query->get("post_type")

Can you try to use this code

 add_action("pre_get_posts", function ($query) {
    if ($query->is_main_query() && is_admin() && in_array($query->get('post_type'), array('company'))) {
        $s = get_search_query();
        $meta_query = [
            'relation' => 'OR',
            [
                'meta_key'     => '_company_inn',
                'value'   => $s,
                'compare' => 'LIKE',
            ],
            [
                'meta_key'     => '_company_phone',
                'value'   => $s,
                'compare' => 'LIKE',
            ],
        ];
        $query->set("s", $s);
        $query->set("meta_query", $meta_query);
    }

    return $query;
});