I think I figured it out issues with Nitrado.
Issue #1: Manually stopping the server and manually starting the server prevents it from actually showing up in the game.
Root cause: Not sure if it's Nitrado-specific issue or an Empyrion bug but certain steam api64 dll files aren't loaded for whatever reason. You can see this in the Nitrado website's "Logs" section.
Solution: After you manually hit "Start Server" and it's allegedly running, hit "Restart server" and it'll pop up.
Issue #2: Game settings and gameoptions.yaml never "apply." It doesn't matter how much you edit settings through the Nitrado website, or download > edit in Notepad and > reupload, it'll never work and settings will never "stick."
(Probable) root cause: Nitrado's auto-generated gameoptions.yaml (located in empyrion > Saves > Games > DediGame) is formatted incorrectly. It shows up as literally two very long lines of text and contains curly brackets example: { and }.
Solution 1a: upload your own gameoptions.yaml with the correct formatting. I've attached my gameoptions.zip for you to work off of. It's 80 lines long. When you do, you have to follow these exact steps:
1. While the server is running, upload gameoptions.yaml into the empyrion > Saves > Games > DediGame folder.
2. Hit "Restart server" in the Nitrado panel.
Solution 1b: If the above doesn't work:
1. Choose Stop Server via Nitrado website
2. Choose Start Server via Nitrado website
3. Upload gameoptions.yaml into the empyrion > Saves > Games > DediGame folder
4. Choose Restart server via Nitrado website.
Note: In other words, keep uploading gameoptions.yaml and choose "Restart server" until it works. lol
Issue #3: Can't warp to another planet in the solar system even though it uses Pentaxid and you're brought back.
Root cause: TimeoutBootingPfServer: 180 is too short of a window of time for the game and server to generate the playfield.
Solution:
1. While the game server is running, go into the dedicated.yaml file via Nitrado located in the main "empyrion" folder.
2. Edit TimeoutBootingPfServer from 180 to 2000 (via the Nitrado site).
3. Be sure to re-upload gameoptions.yaml from Issue #2.
4. Hit "Restart Server".
Note: After restarting, the game will be correctly set to 2000 but you'll notice it'll still show 180 in the Nitrado file. lol
Issue #4: This is likely a Nitrado-specific issue. Every morning, it auto-restarts the server around 5:30am EST. Settings are reset upon server restart.
Solution: You simply have to re-do the above steps daily until Nitrado and/or Empyrion fixes it. lol