MySQL Workbench: v8.0.13
MySQL: v5.7 (installed by brew on macOS 10.14.13)
Server variables tab, everything looks as expected, the options file (my.cnf) has the same settings.
Actually this is how it behaves. eg. character_set_results switches back to utf8 instead of utf8mb4.
Why are the two views different? What causes the difference?
https://dev.mysql.com/doc/workbench/en/wb-mysql-connections-new.html says:
When opening connections, MySQL Workbench automatically sets the client character set to utf8.
You can execute SET NAMES utf8mb4
after you open a connection in MySQL Workbench.
This has been the subject of a bug report against MySQL Workbench:
Bug #78503: MySQL WorkBench's Encoding is Hardcoded to UTF-8
I suggest you go log into that page and click the "Affects Me" button to register your interest.