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julo - I think we're all confused - cover generation is a function of editing the metadata, not conversion - I wasn't aware it came into play with conversion.
I tend to worry about covers after doing any conversion. Since I did my initial upload to calibre, I've not used the cli programs very much, which was well before the new generate cover facility was implemented in metadata edit..
Does your batch file include ===>>>
ebook-meta. If you set the cover generation settings as you want them in the Edit Metadata GUI (e.g. one colour, one style, and check the
Save as default option (bottom left), maybe it will honoured by the ebook-meta program. If it doesn't then maybe ebook-meta needs another option "generate-cover'. You can make a formal request here ==>>
Bugs : calibre
BTW 1: I noticed the blog page you posted suggests putting the batch files in the calibre directory. That is not a practice I would recommend, if you ever needed to do a clean reinstall of calibre (and it does happen from time to time) then you'd lose your scripts.
BTW 2: I don't think you can run the Generate Cover PI from the command line.
BR