many many years ago i worked at a huge bakehouse in Australia.
as the baking pans are being subjected to intense heat, they are baked clean... of course they dont look clean, but you would be hard pressed to find anything other than living yeast bacteria on them.
think of it like a healthy garden.. you can either go organic and have no pests, or you can use chemicals and be forever finding ways to keep the pests off your garden while not causing toxic chemical contamination.
the good bacteria will limit the bad bacteria.
personally i was kind of disgusted at the amount of what i consider to be "built up gunk" on the conveyor lines in the ovens and coolers, but nevertheless we never hear of anyone getting food poisoning from fresh bread (celiacs not included of course).
the oven and cooler racks were cleaned about once every 3 months.. simply by using air jets to blast the lumps of old green floury gunk off the shelves.
even now 25 years later i still dont each much bread, not because of what i thought was unhygienic. but because of the smell of bread... when youve smelled a million loaves youve smelled them all.
the important consideration is that the HACCP process suits the product, and it is not possible to use the same process for vastly different products, good product knowledge is required to understand the nuances of the quality system that is used.