This is an extension to DbContext. Where it only adds Configurations that are DbSets in the DbContext

ModelBuilderExtensions.cs

    public static class ModelBuilderExtensions
    {
        //Only add the IEntityTypeConfigurations that are in the DataContext
        public static void ApplyConfigurationsForEntitiesInContext(this ModelBuilder modelBuilder)
        {
            var types = modelBuilder.Model.GetEntityTypes().Select(t => t.ClrType).ToHashSet();

            modelBuilder.ApplyConfigurationsFromAssembly(
                    Assembly.GetExecutingAssembly(),
                    t => t.GetInterfaces()
                        .Any(i => i.IsGenericType
                            && i.GetGenericTypeDefinition() == typeof(IEntityTypeConfiguration<>)
                            && types.Contains(i.GenericTypeArguments[0]))
                );
        }
    }