A lot of comments about metros areas and the like, such as how Jacksonville shows up because of city limits being larger than atlanta, but if you start getting I to trying to define what a city's metro area is, you run into a lot of issues with giant powerful cities like NY. Can you really count the population of Newark, New Jersey as part of NYC, NY? Even though newark is firmly within the NYC metro area, it's a sep…
You can also define a region as an area of (relatively) continuous density - the Census does this and labels them "urbanized areas". Any one of the 3 approaches (administrative boundaries, commuting zones, density) can be reasonable, depending on what sort of questions you'd like to answer.
> Can you really count the population of Newark, New Jersey as part of NYC, NY?
If you're looking at metro areas (which are defined by commuting regions), then you definitely should, because a sizable fraction of the residents of Newark and the surrounding communities commute into NYC for work. The Census does define a sub-unit called metropolitan division, and Newark, NJ is one of these.
> Is San Francisco part of san Jose?
If your unit of analysis is MSA, then no - "San Francisco-Oakland-Hayward, CA" and "San Jose-Sunnyvale-Santa Clara, CA". This division recognizes that the two have separate (but overlapping) commuting zones - very few people commute from Richmond to Sunnyvale, or from Milpitas to San Francisco.
However, they are both within the "San Jose-San Francisco-Oakland, CA" Combined Statistical Area, which is a broader unit which recognizes that there are commuting relationships between the two areas - they are just weaker than the commuting relationships within the MSAs.
> What about twin cities, like dallas and fort worth?
Dallas-Fort Worth-Arlington, TX is an MSA. For the purposes of maps like this, you can generally just take the name of the city that come first in the MSA name and people will understand what you're referring to.
This slide deck from the US Census Bureau is pretty interesting for understanding their geographic taxonomy, and the trade-offs of different levels of observation: https://www.census.gov/content/dam/Census/data/developers/ge...