The biggest difference is ports. Alaska contains the major port city of Anchorage, which alone (exclusive of suburbs) contains about 40 percent of the state population and over three times the combined population of the Yukon and the Northwest Territories. Alaska's Pacific coast also has numerous smaller ports. Something like five sixths of Alaska's population lives by the coast, with over two-thirds in the Anchorage-Kenai peninsula region.

Conversely, the Yukon and the Northwest Territories are effectively landlocked and have no ports. Although the main gold fields of the Klondike Gold Rush were in the Yukon, most of the prospectors came via ports in Alaska such as Skagway and Dyea. Those who tried to use overland routes on Canadian soil had a very hard time. The Yukon is reached primarily by road (built by the Americans to reach Alaska, incidentally) or air. The Northwest Territories similarly lacks ports. There is simply nothing in either territory similar to the Anchorage-Kenai peninsula region.

To put this another way, the Yukon and the Northwest Territories are somewhat like the Alaskan interior and are similarly empty. Like if you made coastal Alaska from the Panhandle to the Nome peninsula into a different state called Aleutia or something, the remaining inland Alaska (centered on Fairbanks) would probably have a population similar to that of the Yukon or Northwest Territories.