After investigating, this is by design. Recently, there was a change to make the Editor throttle when the app is deactivated, even if the game is running. This is to conserve resources for other activities on the computer.
This change also was to make the behavior standard with macOS and Windows which drop frame rates even more than on Linux with this update.
There is no setting to reduce the throttling in the Editor, but if you need the game to run at full speed in the background for whatever reason, you can build a standalone player and run that way unhindered.