Hi Nathan,
Very interesting post. There's a lot of ground that be covered in discussing your question as to what's preferable to deal with from a food safety point of view. So much depends on the product/risk level, use of dedicated vs. non-dedicated processing equipment, regulatory laws where your company operates, and on and on.
Personally I view both allergens and pathogens to both be huge issues. Either can be the root cause of recalls, or even worse - adverse health effects of our ultimate customers - the comsumer. In the U.S. allergens can be particularly difficult and frustrating to deal with in my industry, basically dry foods with many, many finished products, five allergens, and non-dedicated processing equipment. Wet cleans are somewhat of a negative in that they introduce water to a low water activity process which can result in pathogen issues. However carryover is also an issue with allergens, and a number of steps need to be taken to reduce risk of introducing an allergen from a previously run allergen containing product into subsequent product that doesn't contain that/those allergen(s). Cascading scheduling is one way that this issue can be addressed (after a thorough wet clean, schedule (for example) a non-allergen product, then a product with one allergen (ex. wheat), followed by a two allergen product (ex. wheat and egg), and so on until the processing equipment needs another wet clean due to product buildup that exceeds the SSOP limit.
Pathogens are, as pointed out, a completely different animal (no pun intended). Different preventive measures need to be considered, such as supplier approval (risk analysis that would include supply history, odds of microbial contamination of an ingredient, etc.), random testing of at-risk raw materials, a testing program for finished goods that may be considered by risk analysis to possibly carry a high micro load, etc.
Anyway, good subject and ultimately both allergens and pathogens are huge issues for the food industry around the globe.
Regards,
esquef