AWS Shield Advanced with Route 53

I think it'd be worth reaching out to your local AWS Solutions Architect and/or account team to discuss your requirements here.

However, to answer your question: Shield Advanced covers all of the services you mention. If you're going to enable it, you wouldn't just enable it for Route 53 (and that's not quite how it works in any case). it covers your entire workload.

Just because the authoritative DNS for an AWS resource is on Route53, does not mean the resource is 'behind a Route 53 Hosted Zone'. That's not how DNS works.

You need to enable Shield Advanced Protection for each resource that you want enhanced detection, mitigation or cost protection for.