I think you may have misinterpreted 4.9.1: Processes shall be in place to manage the use, storage and handling of non-food chemicals to prevent chemical contamination.
Clauses 4.9.1 through 4.9.6 are primarily about controlling things that aren't supposed to be in the product
In terms of more general requirements relating to pesticides, mycotoxins, legal use of additives etc, these would be shared amongst several clauses/areas - obviously a significant part is about sourcing the correct raw materials so sits in 3.5, but of course product development is also somewhat key when it comes to the additives element in terms of what is permitted in products, what maximum levels are etc.