Dear JoyceAdmiral,
I somewhat avoided too much detail in my first post due lack of knowledge yr process.
I deduce that basically yr queries refer to the
HACCP-handling of the BCP composition / raw material receiving step.
The fact is that the use of the prerequisite (raw material receiving step) methodology was (partly) introduced to act as a generic solution to accommodate queries as per yr pesticide question via a raw material specification, the latter is compiled on safety / quality logic. Originally this procedure was not routine (I don’t use it myself) but now is near standard vis-à-vis Codex etc (ie auditors like it since it avoids nasty technical questions and (their) time = money). This prerequisite approach also conveniently avoids involving
CCPs for raw material input failures, the scientific basis is perhaps debatable but the pragmatism probably not

.
So yes, the chemical factors like pesticides may be relevant – a prerequisite supplier factor as per yr, mutually-agreed, specification.
And yes again, microbiologically speaking, the official minimum heating requirements assume a certain level of "contamination" if you go into their derivation (the detailed maths are googlable and also linked on this forum somewhere.
I have (rarely) encountered the situation you mention where the normal cooking treatment simply failed to reduce the Salmonella level below detection in the end product necessitating a reprocess (very, very poor raw material). If you look at the US, low acid, canning regulations, you will see a caveat something like “the specified heat treatment may not be appropriate for materials with unusually high bacterial loads / certain matrices”.
From memory, toxin risks from species like Bacillus are controlled via the appropriate, designated post-heating cooling. Nonetheless, an absolute level is similarly usually specified in the (prerequisite) raw material spec. again.
If you are interested, there is a lot of technical explanations regarding the, especially microbiological,
haccp-oriented specification of raw materials such as discussed here in the publications of Snyder (
http://www.hi-tm.com ). These analyse what cooking process (heat etc) is necessary to (safely) match certain target (usually Salmonella) bacterial input level. But I daresay you are aware of a lot of this already.
Rgds / Charles.C