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.

For transfer setting, you can pre-configure your preferred settings as default transfer settings. The script uses the default transfer settings as initial.

You should then isolate configuration prepared for the script.

If the value of the option is not static you can generate the INI file before running the script.

For example, to configure changing case of filenames to lowercase during transfer, use following INI file:

[Configuration\Interface\CopyParam]
; File name case modification (1 = Upper case, 2 = Lower case, 4 = Lower case 8.3)
FileNameCase=2

The same applies to most other settings, such as configuring reconnect interval:

[Configuration\Interface]
SessionReopenAuto=10000