Do developers create games at a specific resolution, and upscale or downscale depending on the monitor? It seems that the Just Cause 2 PC game was originally made at 2560*1600, while others were made to play on a console, we get the port, and the pixels are just stretched to fit the screen. Is this true?
Resolutions do not work that way. 3D Games are not made at any particular resolution. Aspects of the graphics can be made with a particular resolution in mind (as in, "these textures are good enough - they'll never notice how bad they are since it's going to run at 1064x600"), but ultimately, the actual graphics are made up of vectors, which have basically infinity resolution. When you actually play the game, these vectors become rendered into a grid of pixels, the size of the grid being whatever resolution you selected.
And I third everyone saying that Kane & Lynch 2 is not "upscaling."
I haven't tried Kane and Lynch but if you can select 2560*1600 in the options there should be no upscaling what so ever. That goes for all the games you listed and some 98%+ of 3d games that came out in the last 5 years.
Actually, I do not think there has ever been a single 3D game on PC that works by upscaling to your native res. So I'd say that goes for 100% of 3D games that came out in the history of everything.