As it was said in a comment on this question -- bookdowns gitbook does not propagate things like \newcommand that work fine for the pdf_book output.
Is there a better workaround than moving the \newcommand to the first chapter's 01-intro.Rmd markdown file? This works but it somehow messes up the clean markdown syntax.
Or is there even a fix for this issue? (I didn't find anything related in the bookdown issue tracker)