You can configure initial directories of a session the same way as always:
https://winscp.net/eng/docs/ui_login_directories

What has changed, is that the main window now opens even before you open the first session. It opens a with local folder in which the application was closed the previously (if you have the very latest version of WinSCP).

Earlier versions used to allow me to specify what directory I wanted the app to open in upon startup (both in the root and remote locations). Am I missing that preference setup or did you do away with that? Please advise and/or put it back. Thanks