The cacao/cocoa powder (or nibs) is completely optional. It may make the toothpaste more appealing to kids. It also may leave dark marks on the sink if not fully rinsed. Choose whether or not to add it accordingly.
Theobromine in cacao may help with remineralization.
DO NOT use xylitol for toothpaste meant for pets. It is toxic to dogs and cats and possibly other animals. If you plan on making a toothpaste for a pet, I'd suggest not using sweeteners or essential oils.
Because this toothpaste has water in it, it has a shorter shelf life than the the oil-based toothpaste. It is self-preserving due to the high pH and the addition of salt. Making substitutions to the ingredients could make it prone to microbial growth.
Be careful not to contaminate the toothpaste with bacteria. Do not dip your toothbrush into a jar of this toothpaste to avoid contamination. Instead, either dispense the toothpaste from silicone tubes or scoop out just enough for one use with a clean spoon or other utensil.