Answering my own question, sort of. Using "doit.log" 's generated command is
actually extremely easy. It's a useful way to set the settings using the GUI,
but then run them via the command line (and potentially using a cronjob to run
on a schedule or something like that).

I still don't know exactly what that beginning string is for - I imagine it's
some kind of serialization - but I just run the executable without that and it
works perfectly. Another great experience using HTTrack!