I work at a SQF-certified Level 3 facility, and all we make are blowmold bottles and jars (except ours are for hotfill juice and applesauce). We are strictly category 27 in SQF, which means we only follow Modules 2 (System Elements) and 13 (GMP's for Food Package Manufacturing).
It could be argued that, even though you are not selling your bottles to outside customers, they are a part of your product (a food ingredient, if you will). I would compare module 13 to the modules you are currently certified under and see if there are any discrepancies you may need to address.
However, I'd say the easiest solution would be to ask either your certifying body or SQFI itself what is the proper thing to do in your specific situation. It would be best to find out now then to have an auditor bring it up at your re-certification as an issue.
"Imagination is more important than knowledge. For knowledge is limited, whereas imagination embraces the entire world, stimulating progress, giving birth to evolution."- Albert Einstein