Opening session using command-line parameter in scripting is deprecated.
Are you aware of what that warning exactly means?
It says that you should not do
winscp site /command commands
winscp /command "open site" commands
It does not limit you anyhow.
It just warns you that you are combining features that were never intended to be combined.
Also, we are definitely not intending to remove the ability to load stored sites in scripting (although we discourage it).