Not sure if you have abandoned the part of yr OP related to 188.8.131.52 but as far as i can see it requires "Procedures". The Checklist would appear to be an additional issue.
As per the format shown, the Guidance for 13.4.1 includes all of subs 1-3 but i agree with you that the list of "evidences" shown is contradictory.
Sadly I could not find any forum comments relating to 184.108.40.206 from other SQF Packaging users. Perhaps they simply ignored it. Dot2 does not appear to exist in any other modules so perhaps the author of (13) decided to add it as a novelty.
Additionally one must always remember that the Guidance is only a non-binding "suggestion", albeit a tantalising one.
The auditor has the final word.
Well, After a bit of back and forth this was what we received a NC on for GMP
Our actual finding listed below.
220.127.116.11 Food Safety Management
Item: A food Safety Manual shall be documented, maintained , made available to relevant staff and include or reference the written procedures, pre-reqs, food safety plans and other documentations necessary to support the development and the implementation, maintenance and control of the SQF System.
Evidence: The company has documented a Quality Manual (Quality-002) which outlines the methods used to meet the requirements of the standard. Some programs needed to maintain the SQF Management System were not documented such as management review.
A list of pre-reqs was also included but it was noticed that not all programs are referenced such as Personal practices/GMP, control of chemicals, Monitoring of water and air quality.
So now I am sitting here wondering exactly what is supposed to go into a GMP pre-req. The standard to me isn't clear at all.