Actually, having worked in a few (bakeries, I mean)-- the risks are really pretty similar, IMO. It just really, really depends upon the individual establishment.
The small shop that I worked in was meticulous from a cleaning/sanitizing standpoint. We hand-washed most trays and dishes, and used single-use disposable tray liners on top of THAT, and no way was a mixing bowl or counter used with just a wipe-down in between product.
On the other hand, in the higher-volume supermarket bakery that I worked in, everything was cross-contaminated in nightmarish, myriad ways. EVERYTHING.
Most people would have anticipated that the larger, higher-volume place affiliated with a major supermarket chain would have had WAY better "protocols" etc, but it was definitely not so. So sure-- we could provide labels in a way that the smaller place would have struggled to do... but the risks were still at least an order of magnitude higher. Cleaning happened infrequently between product, re-work was commonplace, open/shared rack space was common, parchments were re-used in oven tray racks, etc. etc. etc. etc. It went on and on and on. NONE of that stuff was a food-safety risk-- in fact, in a general health-department kind of way, the two shops were very good and on equal footing. But from an allergy stance, there was no comparison.