The depictions of populated areas on aeronautical charts have never been intended to define minimum altitudes with respect to 14 CFR 91.119. Never rely on depictions on an aeronautical chart to justify your separation from objects, obstacles, or persons.
91.119 does not refer to densly populated areas, but congested areas. It also refers to sparsely populated areas. Formerly, the regulation spoke to built-up areas. Specifically, today, 91.119 identifies congested areas as cities, a town, a settlement, or any open air assembly of persons. Yes, one or two houses constitutes a settlement and qualifies for increased separation, as does a gathering of two or more persons.
Aeronautical planners make a general attempt to roughly define the shape of the city when depicting large populated areas on aeronautical charts. Because these areas are lighted at night, this will generally conform to the basic shape or outline of the populated area. However, no attempt is made to be exact, or specific, and one should not expect to see the same thing on the ground that one sees on the chart. Population centers change, power outages occur, etc.
The yellow on the chart is strictly to show a population base as a reference. It shouldn't be used, or implied in use, in any other context.