Dear Syju ,
OK , yes you can , in the scope of the pre-audit /certificate questionnaire you determine your selected scope , e.g. line X facility Y for product C accordingly the audit and certificate will be issued with these data declaring the exact scope ,it is done for ISO 22000 also , but I think this is not fair for the organization , especially when you are dealing with a by-product this means that the main process will be audit to assure that the resulted product , even if it is a by-product , is complaint , this means that you will do efforts more with limited certificate . I prefer if the main processes / facility requires some efforts do it and get full certificate this is better for your quality /food safety .
for reference please review
http://www.fssc22000...2-v3.1_2014.pdf
review page 5 and page 6
Design of the certificate
"scope, expressed in terms of categories, sectors, production processes, products and sites;.............................................................."
hope this covers your point.
good luck ,
Ehab