Application Gateway behind Front Door is useful in these situations:
You want to balance the traffic not only globally, but also within your VNET. Front Door can only do path-based load balancing at the global level, but Application Gateway can do it within your VNET.
You need Connection Draining, which Front Door doesn't support. Application Gateway can enable Connection Draining for your VMs or containers.
You want to offload all the TLS/SSL processing and use only HTTP requests in your VNET. Application Gateway behind Front Door can achieve this setup.
You want to use session affinity at both the regional and the server level. Front Door can send the traffic from a user session to the same backend in a region, but Application Gateway can send it to the same server in the backend.