Learn Italian: Dopo che la strega ebbe bevuto la pozione, trasformò il re. - After the witch had drunk the potion, she transformed the king.

Because the main action trasformò is in the passato remoto, which describes a completed action in the distant past, and it is introduced by the time phrase dopo che (after). When you want to say one distant past action happened immediately before another, the earlier action requires the trapassato remoto.

Could we just use 'ebbe bevuto' on its own to say 'she had drunk' in a simple sentence?

No, the trapassato remoto is virtually never used as a standalone verb in a main clause. It acts as a supporting character, used almost exclusively in dependent clauses starting with time expressions like dopo che, appena, or non appena, simply to show an action finished right before the main passato remoto action began.

How exactly is the verb form 'ebbe bevuto' built?

It combines the passato remoto form of the auxiliary verb avere (which is ebbe for the third-person singular) with the past participle of bere, which is the irregular form bevuto.

The English translation says 'she transformed', but there is no pronoun before 'trasformò'. Why?

In Italian, subjects are routinely dropped when the context is clear. Since la strega was already established as the subject in the first part of the sentence, it carries over naturally to trasformò. Adding lei here would sound clunky or overly emphatic.