hopefully this is not known till now. I haven't found anything about that.
Version: 5.13 Build 8172
Windows 10 Pro 1709
Link protocol: ssh
Interface Style: Commander
Steps: open WinSCP, connect to a Server. If the connection is established, use a browser with a ssh link to open terminal. it now will open two windows insted of one.
(If WinSCP GUI is not opened it only starts one terminal/putty window)