quot;take the pizza out of the box and put it on the

Pronouns that may seem ambiguous at first can be considered clear if the structure of the sentence clues you into the intended antecedent.

The structure of the sentence is "Take the pizza (out of the box) and put it (on the table)"

There are two parallel prepositional phrases here-- "out of the box" and "on the table"--these phrases tell you where you are "taking" and "putting" the pizza, respectively. These are modifiers, and you can ignore them both when examining the deeper underlying structure.

Ravsg, you're right that "you" is implied, and pizza is indeed the direct object. It answers the question "what should you take?."

So the core structure here is really IMPERATIVE TRANSITIVE VERB (take)-OBJECT (the pizza) AND IMPERATIVE TRANSITIVE VERB (put)-OBJECT (it)

That parallel structure tells us that "it" refers back to the word in the same structural/functional slot (OBJECT), or "pizza."

Hope this helps.