The Calibre version has a command line option, just use "comic2lrf". All the options in the GUI are available in the command line version. I never use the GUI either
You need v0.4.84 for the "full resolution in landscape" option. Also the "--despeckle" option is worth using all the time to clean up those grainy comics, if you've got a decent Processor.
I've no idea when Kovid will release v0.4.84 but you could use the beta version which looks pretty stable now:
http://calibre.kovidgoyal.net/downloads/betas