There are only so many fish available for stocking. If they are spread the around the entire lake then they would be too spread out to create any fishery of note. By putting them in one spot, they can create a local fishery. Despite it's reputation, Hamilton Harbour does have good habitat to support walleye reproduction.
Going forward, they will stock Toronto in odd numbered years (100,000 in 2017) and Hamilton in even numbered years. Perhaps they will eventually establish fisheries around the lake.