Terminal Emulator option does not output log files in another window

when editing your configuration settings, you are able to emulate console output in a terminal window, but this limits a lot of the functionality, which somewhat makes sense if PyCharm is just forwarding the console output to a terminal window or something along those lines.

What I am confused by is that after selecting the option, I can longer output log files in separate windows as my incoming streams are logged.

Is this something that is an issue, purposeful design, or am I missing something.