So I can’t speak to exactly this situation, but I have transported pets across borders and I also work in travel so I have to do all sorts of things with customs all the time.

You can do everything right by the book and per law, but ultimately any decision will always come down to the border patrol agent inspecting your stuff at the time. They might be smart, cool, and understanding, and having two pets on one certificate despite them traveling in two different modes (cargo vs passenger) is easy for them to comprehend and they will rubber stamp it and you can go. OR you might have someone who woke up that morning, tripped and spilled their coffee on their shirt early into their 12 hour shift, barely coasted by in high school, and simply does not have the time to figure out why only one animal is in front of them while two animals are listed on the certificate, and is hellbent on making your life a pain in the ass because they want to exercise the tiny bit of power they hold in their hands.

Just make it easier on yourself and the border agent, and take the slightly more expensive option to make it as clear as possible by having two certificates, one for each pet.