All the option classes are still available, have you tried:

services.Configure<OpenIddictServerOptions>(options =>
{
    options.Handlers.Add(new OpenIddictServerHandlerDescriptor
    {
        ...
    });
});

There is probably an extension method available to make this code nicer, so you don't have to construct the descriptor. It also look like you have to add the descriptor to the container:

var descriptor = new OpenIddictServerHandlerDescriptor
{
   ...
};

services.Add(descriptor.ServiceDescriptor);

services.Configure<OpenIddictServerOptions>(options =>
{
    options.Handlers.Add(descriptor);
});

I've added to our backlog that we should look into exposing OpenIddictBuilder, which makes the code a bit cleaner when you want to extend our code.

Thanks, works like a charm!

+1 if it could be exposed as part of the Episerver package.