In more simple terms, did the Duwamish and Suquamish tribes have their larger settlements where Seattle and Bellevue are? The same for Kitsaps with Bremerton, Puyallups/Nisqually with Tacoma, Squamish/Musqueams with Vancouver, etc? If there were significant differences, why did things develop differently when the Europeans arrived?
Great question, and really pertinent too, as lots of scholars focused on Indigenous histories are increasingly looking to geography and, specifically, GIS technology to enhance historical analysis.
From what I've read, yes, generally, prominent Indigenous villages tend to overlap with European settlements, especially in the area of the Salish Sea.
For instance, from Simon Fraser's account of his voyage down the river that now bears his name, we know that he and his men stopped in a number of Coast Salish villages after leaving Nlaka'pamux territory. Comparing this data with subsequent reserve creation, and then correlating it again with reference to contemporary urban centers, we can see that Ts'elxwéyeqw lands became a series of small reserves, around which the city of Chilliwack and town of Sardis have subsequently been built. The same is true for Katzie villages in the area of New Westminster, and of course Musqueam centers in what is now Vancouver. Or, take the town of Mission, also on the Fraser River, which was established by Catholic missionaries because many Coast Salish people lived, met, or traded in that area.
On the other hand, of course not all significant village sites have become contemporary cities; for instance, a former rock wall fortress surrounded by house pits called Xelhalh, which was clearly a prominent Stó:lō site has, as Wenona Victor explains, "somehow escaped White settlement and encroachment." Victor goes on to describe walking through the archaeological remains at the site as "very much like walking through a ghost town." See Victor, "XeXa:ls and the Power of Transformation," (PhD dissertation, Simon Fraser University, 2012) 165-166. Link to PDF here.
Lots of historians have done great work on this topic. I urge you to check out these titles for more specific information:
Carlson, Keith Thor, ed. A Stó:lō-Coast Salish Historical Atlas. Vancouver: Douglas & McIntyre, 2001.
Harris, Cole. Making Native Space: Colonialism, Resistance, and Reserves in British Columbia. Vancouver: UBC Press, 2002.
Thrush, Coll. Native Seattle: Stories from the Crossing-Over Place. Seattle: University of Washington Press, 2007.