How do I configure site, transfer and/or any other settings for which there are no script commands?

For site settings, you can use -rawsettings switch of open command.

See raw site settings syntax. WinSCP can generate the code for you.

For transfer settings, use -rawtransfersettings switch of script commands that transfer files, like put, get, synchronize, etc.

See raw transfer settings syntax.

For global settings, use /rawconfig command-line parameter.

See raw configuration syntax.