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My bad, I gave you an incorrect refactoring example for your case.
It should have been something like the following and it would be totally fine (I can spot a lot of other bidders that do similar things you try to do)

    private static Site modifySite(Site site, String id) {
        return Optional.ofNullable(site)
                .map(Site::toBuilder)
                .map(builder -> builder.publisher(modifyPublisher(site.getPublisher(), id)))
                .map(Site.SiteBuilder::build)
                .orElse(null);
    }
    
   private static Publisher modifyPublisher(Publisher publisher, String id) {
        return Optional.ofNullable(publisher)
                .map(Publisher::toBuilder)
                .orElseGet(Publisher::builder)
                .id(id)
                .build();
   }            

But If you'd like to set the siteId to another target request.site.publisher.ext.prebid.publisherId I can suggest adding a publisherId property to the ExtPublisherPrebid class - but you have to make sure other bidders that uses the same class will be able to compile and the tests will pass after the changes