There may be a minor difference in the ink mix. All spot colors are "mixed" using a formula an ink mixer uses to match the spot color on press. The "swatch" itself may be the same percentages between the two, but the difference is identifying the type of spot color which will show up on plates when the file is separated to direct-to-plate setter.

Most spot colors are opaque, whereas 4c process inks are semi-transparent. In some cases, depending on the colored paper, an apaque White may need to go down first because the spot color is spec'd using a White paper stock. So, in order to keep the color's true color intact, it may have to go over a white. Pantone metallics look good on colored paper, but sometimes they need a double-strike to hold up on some dark colored stocks.