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
open 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