In the file, it stores "This item is pantone-1234", and lets the software using the file figure out what to do with it. So when it's rendered to screen, it uses a lookup to pick a good RGB color. When it's printed in CMYK it uses another. When you check it against what light it reflects, that's it's own set of rules about what it's "supposed to" look like. Fancy industrial printers have the ability to load specific inks for specific colors. So a press might support 4 colors, which you normally load CMYK. But let's say you're making a bunch of pamphlets for one company, which is black and white, but they want their logo on each page. You can load Black, and 3 other customs colors in instead. Some machines support something like 8 colors, just for this reason. Sometimes you need to load white ink because your printing on non-white materials. CMYK is just the most basic way of printing color.