When following the hay diet, learning the nutrition advice the creator gives is a smart way to help yourself understand why you are eating this way.
The nutrition advice he gives for the digestion of protein in combination with starch is that when you consume protein rich foods with starch rich foods there is going to be too much acid in the body to allow for the alkaline reduction that's required to digest the starch containing foods. Then, there will also be too little acid present to kickstart the digestion of protein.
To explain this nutrition advice on a deeper level, first you need to look at the digestion of protein. When the body is digesting proteins you need hydrochloric acid present in order to activate an enzyme called pepsin. Pepsin, once activated, will then start splitting and digesting the proteins, however this process needs to take place in a very acidic environment. If it is being neutralized by the presence of foods that are high in starch or sugar (as these are rich in alkalies), then the protein digestion will not be complete and you will likely suffer from indigestion and a potential malabsorption of the proteins.
Because the body requires proteins to repair old body tissues and generate new ones, this is very problematic and is definitely not a good way to promote overall health.
Once you understand how this process works, then maybe it will make your motivation to avoid eating starches and proteins together higher. This then will definitely help you with following the principles laid out in the program.