I think I found the answer to my Canada Customs question on the Canadian Food Inspection Agency's website.

It appears that if a valid rabies certificate isn't presented at the port of entry, the inspector will order the owner to have the animal vaccinated within a specified period of time and then present the certificate.

I will likely still get the rabies vaccination done in advance, but it's good to know the policy.

I'd still be interested in knowing whether AC allows people to book an extra seat (in general, not necessarily just in the traveling-with-a-pet situation) and if so whether it can be done online.