You've got 2 separate sections of the code confused--you rightly got dinged because proficiency testing is required for ALL internal lab testing
2.4.4.2 Product analyses shall be conducted to nationally recognized methods or company requirements, or alternative methods that are validated as equivalent to the nationally recognized methods.
Where internal laboratories are used to conduct input, environmental, or product analyses, sampling and testing methods shall be in accordance with the applicable requirements of ISO/IEC 17025, including annual proficiency testing for staff conducting analyses.
External laboratories shall be accredited to ISO/IEC 17025, or an equivalent international standard, and included on the site’s contract service specifications list (refer to 2.3.2.11).
2.4.4.3
On-site laboratories conducting chemical and microbiological analyses that may pose a risk to product safety shall be located separate from any food processing or handling activity and designed to limit access only to authorized personnel.
Signage shall be displayed identifying the laboratory area as a restricted area,
accessible only by authorized personnel.