One isn't necessarily more nutritious than the other. They're just different foods. Peanut butter comes from a legume and almond butter comes from a tree nut, but nutritionally they're fairly similar. Both provide mostly healthy fats along with a little protein and fiber.
He explains, "Look for frozen pizzas with fewer additives - avoid dough conditioners in the crust and anti-caking agents like cellulose in the cheese." Anti-caking agents are additives used to prevent shredded cheese from clumping or sticking together. Sometimes, the agents are cellulose (or wood pulp) and other times, it's cornstarch. Anti-caking agents can interfere with how the cheese melts and browns, which is something pizza purists like Gemignani prefer to avoid.