I recently reported this (to the bot's owner who reported it here) and I was surprised that the Lojban Wiktionary was the first wiki to opt out of this, when the much larger English Wiktionary has the same headings convention. Looking through some of the pages changed, I think that the cosmetic changes were just automatically reverted by people's clean-up bots and it wasn't really noticed that a few bots broke that convention. Anyway, if this was applied to the English Wiktionary too I think we wouldn't have to worry about a subtle bot war under the bed :)
rPWBCbc0124291e9b: [L10N] Disable cleanUpSectionHeaders on jbo.wiktionary was for jbo.wiktionary indeed. I'm not sure if adding "wiktionary:en" next to wiktionary:jbo: will fix it as I'm not a pywikibot coder though, but looks easy to fix to me.