When running the commands "/whitelist add Tis_awesomeness" or "/whitelist add jeb_" while the players are not online, the server responds with "That player does not exist" instead of actually adding the player to the whitelist. This also happens when running /op instead of /whitelist.
I and a few others tested the commands on vanilla online-mode 1.16.5 servers (though it probably affects many versions) and got the same result each time.
Workaround: Manually edit whitelist.json and ops.json
Caused by WEB-4457
As stated in your description, this issue is being caused by WEB-4457. This is due to the api being down and therefore whitelisting not working.
This isn't something that can be fixed within the game and is a problem with the API.