I don't have access to the book mentioned in the OPs question so this answer will be based on the limited information present in the question.
There are many ways in which people "learn mathematics" and many different aspects of what is important depending on the learners focus and scope.
Some don't need to learn the fundamental intricacies of a theorem and instead want to focus on its use towards other things. Others choose to delve deep into those intricacies and find out how the theorem relates to the components it was derived from.
There is one thing in common that both groups need to be sure of however, namely Logical Validity and Soundness. For example for a theorem $A \implies B$ they need to be able to recognize and ascertain the two following conditions to make good use of the theorem.
- The scope in which the theorem is stated. They need to be able to recognize when they can use the theorem and when they cannot. In this case they need to be able to ascertain whether $A$ is true or not for their use case.
- The trust that the theorem has been proved, i.e. trust that there is a valid chain of logical reasoning that establishes that from $A$ you can imply $B$. (That is, whenever A is true then B must also be true.)
With that in mind we can try to answer your questions. Question 1 and 2 uses subjective measures ("worthwhile" and "mastered") so they will also have subjective answers.
1. Was it worthwhile to derive it at time B?
Lets consider the equation here. You've invested time and mental resources to derive the theorem and made sure there are no errors in the reasoning. From this, what have you gained?
In terms of the two bullet points above, you've ascertained that, indeed, there is a valid chain of reasoning from $A$ to $B$. You've also hopefully been able to reinforce your understanding of when $A$ is true and what pitfalls may arise that makes it not true. So you've been able to strengthen your trust in both the validity of the theorem as well as your ability to recognize its scope. This trust is something you will remember.
2. When does automatization happen?
I (the answer writer) can't decisively determine this since I don't have access to the book. So this must be taken with a grain of salt.
However, from OPs own statement:
In the first step, we need clear guidance(verbal control and explicit memory retrieval)
It seems that proceduralization is the activity of explicitly recalling and following the recipe needed to get from the premises to the conclusion.
Automatization seems to be the process of these steps getting internalized and processed implicitly without need of conscious effort to follow them.
Thus I think the answer is that Automatization can happen in any/all of the steps A, B and C.
3. Is it okay to skip the derivation and remember only the theorem?
A theorem that we learn in a mathematics book is itself a "landmark" result in a big forest of logically valid chains of reasoning. They are mentioned because they are noteworthy and useful.
This means that learning only the theorem $A \implies B$ itself is great as long as you are able to trust your understanding of the two bullet points. You don't need to commit the derivation to memory as long as you know the theorem itself holds.
However, if you are tasked with convincing someone else that the theorem $A \implies B$ is true, you need to be able to convince them of the two bullet points. Commiting every single derivation to long-term memory is something that is seldom done but in this case you might need that information. Most people probably remember some landmark steps of the derivation but not every single step.
The theorem itself seems to be an automatization you're talking about if one is used to do every step of the derivation. It is useful to you and for getting the job done. If you cannot give the detailed derivation yourself then, you should maintain a list of references towards the derivations or know how to look them up again. A book or handwritten notes are "memory" too, even if they aren't in your head.