Core Shell/ Tunnel in line with your system ssh command after Core Helper installed, so that you can gain in consistency when you switch between Core Shell/ Tunnel and system ssh command.
That's also true of Setapp version of Core Shell.
But for App Store version of Core Shell/ Tunnel and without Core Helper, things slightly different. Apple requires all apps in App Store been sandboxed, we've explained it in this topic:
Which means by default Core Shell/ Tunnel do not have same privileges as system ssh, and have to read/write known_hosts
inside its own sandbox container as per Sandbox policy requires.
Yang