Human anesthesia gives us a perfect example. If you give someone a sedative before surgery, but not an analgesic – they will lose consciousness, but their autonomic nervous system will still respond to the pain. As the surgeon is cutting, their heart rate and blood pressure will increase, even though they aren’t conscious. The patient won’t care/remember, but the increase in heart rate and blood pressure can make all sorts of surgeries more dangerous, increase blood loss, etc. So even though the patient won’t ever be aware of the pain, an analgesic is typically given.
So, circling back to other animals, whether they be mammals or reptiles – the debate is around what sort of conscious distress they feel. We look at how the human brain responds to traumatic injury and certain drugs and then make educated guesses based on the presence/size of those structures in the animal. Localization of function tells us that brain tissue is specialized to certain activities.