In this example, the cheese is exempted because it is frozen, not because it's mixed with other ingredients. My take on all of the FTL items is that adding an ingredient on the list to your finished product makes your product an FTL item moving forward.
"The additional recordkeeping requirements apply to the foods specifically listed on the FTL, and to foods that contain listed foods as ingredients, provided that the listed food that is used as an ingredient remains in the same form (e.g., fresh) in which it appears on the list."
Food Traceability List | FDA
To the pizza example: if you're creating pizzas with refrigerated cheese and then freezing the whole pizza, you're on the hook to have KDE's for the cheese up until your documented freezing of the product, at which point your can claim an exemption. If you're adding fresh-cut vegetables to your pizza, it too is a traceable item now up until the point it gets frozen (because freezing would change the status of the fresh-cut vegetables to frozen vegetables).
Going round and round on this with two of our plants that make products with ingredients on the list:
First plant:
"We cook the salmon burgers, so we're exempt."
'The finished product is exempt, yes, but you're getting the fish raw so you need to have the KDE's from the shipper and you need to record them at receiving. Then we need to document KDE's at the transformation of raw fish into a cooked patty.'
"But the finished product is exempt!"
'Grumbling noises'
Second plant:
"Our jalapeno poppers are to be cooked by the consumer, so they will undergo a kill-step, and they should be exempt."
'No, your jalapeno poppers have peppers, an FTL item from their harvest, which you cut and create a new FTL item (fresh-cut veg), which you stuff with another FTL item (cheese). These are FTL the whole way."
"But if the bacon we wrap them with is pre-cooked, doesn't that count as a kill-step?"
'How do you...........*eye twitch*..........NO!'