Please follow this manual (which you probably already did?):
Documentation in Research Papers
the formatting becomes absolutely chaotic because the pages have different sizes.
The only practical solution for that usually is do use a fixed with, and split single pages from the online questionnaire on multiple pages in the appendix. Or, if the online pages are small, you may also put multi of them on a single print-page. But, having pages of different length will definitely require some cutting. When doing this properly, you can usually achieve very good results.