By Definitions as per MySQL Reference Manual: utf8mb4: A UTF-8 encoding of the Unicode character set using one to four bytes per character. utf8mb3 : A UTF-8 encoding of the Unicode character set using one to three bytes per character.

Since, utf8mb3 (also known as UTF8) can not store all languages like Chinese or Emoticons, it is recommended to use utf8mb4 when it comes to store application data.

For simple example, You want to extend your existing business into China. if you have used utf8mb4, your application is always ready to adopt your business extension while in case of utf8mb3(UTF-8), you need an character set upgrade to your application.

While storing system's data MySQL does not store information (supplementary character) which requires utf8mb4, this could be the reason, why MySQL itself is not using utf8mb4.