As far as I remember, the terminal window is there for the last 3 years (~30 releases). It was put there when a former colleague working on Molflow removed progressbars and status messages from the GUI in 2.9 - they needed to be printed to the terminal. I’ve put back most, so soon I’ll remove it, good that you reminded.
By the way, we don’t recommend opening multiple instances at the same time, memory is one issue, but config file (for example recent file list) gets overwritten by each instance.