Fine-tuned Inception V3 output tensor shape

I was following the tutorial provided in Tensorflow Slim repository to fine-tune the InceptionV3 model with flowers dataset. I was able to go all the way to the end of the tutorial in terms of freezing the graph and utilizing it in my own code. However, I was under the impression the fine-tuning of the model with change the output tensor from (?, 1001) to (?, 5) shape. But the shape is still (?, 1001). Am I missing something here?

I was testing it out with the flowers dataset, but eventually my goal is to train a model with classes not present in the 1001 from ImageNet.

Any help is appreciated. Thanks.

The official documentation does not provide all the arguments required for exporting the inference graph. Switched from

$ python export_inference_graph.py \
  --alsologtostderr \
  --model_name=inception_v3 \
  --output_file=/tmp/inception_v3_inf_graph.pb

to

python3 export_inference_graph.py \
    --alsologtostderr \
    --model_name=inception_v3 \
    --train_dir=training/ \
    --dataset_dir=/tmp/flowers/ \
    --dataset_name=flowers \
    --output_file=/tmp/inception_v3_inf_graph.pb