More on the onion and the way it grows - does the prohibited part forbid the permitted part, or vice versa? Note the Talmudic, halakhic concept: Davar she-yesh lol matirin - a way to permit something that was forbidden. How that concept is applied elsewhere, especially with regard to mixtures, and here. Also, weeding with a Kuti/Samaritan, who is not considered reliable for taking terumot and maaserot, with implications for shemitah concerns as well. All of these concerns seem to kick in for the kind of bulbs that grow over themselves, as it were, as compared to beans, which are transformed.