That's only if you transport cargo/goods via single modal transportation. Any transportation solution in the North will be multimodal in nature.
Churchill is the only Deepwater port in the North with direct rail access. Heavy equipment and machinery can be transported there, transloaded on to ship for disembarkation elsewhere. St John's is on an island and isolated from the rest of Canada, it's objectively a terrible logistics hub.
There is a Deepwater port in Iqaluit that was just constructed:
It's 800 NM to Iqaluit from Churchill. It's 1200 NM from St John's to Iqaluit. Iqaluit is the busiest port in the Arctic and receives the most cargo of any Arctic community in Canada. Supplying Iqaluit from Churchill seems to be a no Brainer.
Churchill also gives a direct route for raw materials from Western Canada to go to European markets.