Have been boarded, full inspection by DFO after coming in from fishing/prawning/crabbing. Had Ling Cod and Salmon spines/fins/parts on board in my fridge and still pieces in my crab trap bait bags. They didn't give one **** about any of that stuff. Just wanted to see my numbers/sex of crab, size/species of salmon, and number of prawns caught (this was pre reg about female egg baring prawns but we didn't keep any females anyway so they liked that), also checked us for all our safety stuff on board even though we were currently tied up to a marina just after coming in when they checked us and we had everything we were supposed to have on board, even two of some of the safety items so they were very pleased. All the years of fishing on the ocean I've never heard of any DFO giving any fines out whatsoever for using fish carcasses for bait and that's on both sides of the border cause I fished out of Point Roberts a lot a while back. Can't remember if it's written BS like that in the USA regs but they never gave a **** either if it was.
But do as you please and interpret it how you see fit. You're boat, your gear, so no one should take law advice from guys on the internet anyway. If you are that worried about it call DFO, get a name of who you talk to, ask for an email with a reply to your questions and keep it on board with you. May give you the peace of mind you are after about it. I've done this in the past for example with the packaging/transportation reg interpretations..