The SQF Certification applies to the facility/system/and products that you note are included in the scope of certification. Thus your certificate would show what products (or categories of products) are included in the scope.
You can EXEMPT certain products or entire processing sections - this would be handled thru your chosen Certification Body (the company that provides the Auditor an services your certification.
Now the catch is those areas are normally sectioned off (walled almost always) but are still subject to inspection by an Auditor to ensure that there is no cross-over, storage of components the the scope section to the un-scoped section, or storage of foods only used in one section and not the other etc.
Frankly, in my about 20 years doing SQF I audited only a handful of companies that had exemptions and most of our clients did not have exemptions - except for a giant one that exempted 12 buildings on the site - that must have been a fun tour for the Auditor.
You can find all sorts of good stuff on www.SQFI.com
They prefer not be be called - but are quick in turn-around on their contact page...
https://www.sqfi.com/contact-us
All the Best,
All Rights Reserved,
Without Prejudice,
Glenn Oster.
Glenn Oster Consulting, LLC
SQF System Development | Internal Auditor Training | eConsultant
http://glennoster.website3.me/ -- 774.563.6161
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www.GlennOster.com