You should get the warning even with the latest version. I get it, when I try simple:
C:\>winscp.com name /command "exit"
Opening session using command-line parameter in scripting is deprecated. Use 'open' command instead.
In scripting you should not rely on saved sites, use this command instead: open ...
Searching for host... Connecting to host... Authenticating...
In general, the recommended approach is to use the
command. If you want to combine opening the session from command-line and commands in the script, without getting the deprecation warning, you can do this:
winscp.com /command "open name" /script=script.txt