Learn English – The day before/ yesterday…were/had been — forming sentences, trying to convey things concerning the past and the past before past

The basic rule for tense shift in reported speech is"

1 Present tense becomes past tense

2 Past tense becomes past perfect

3 Future tense becomes conditional tense

Direct speech: I do - reported speech: He said he did

I did - He said he had done

I'll do - He said he would do

Why [is the p]ast perfect [...] used here?

Because the main verb of the sentence--disclosed--is in the past tense and the (completed) actions described by the verbs engage and scrap occurred before that disclosure. As has been mentioned, the sentence is not written in the clearest manner possible. That said, its verb tenses are correct and bog standard.

To address the other options:

...had allegedly been engaged...

just adds another layer of opacity to the writing and either means (a) exactly the same thing as the terser phrasing or (b) means that some other entity was responsible for engaging these companies in suspicious transactions. Sense (b) doesn't seem supported by the rest of the context, so it's just making poor phrasing worse.

...were allegedly engaged...

similarly can mean (a) exactly the same thing as the past perfect or (b) shift it into the passive. Again, sense (b) doesn't seem supported. The difference between the first sense and the past perfect is that the same action is being described, but without reference to the occurrence of the main verb. It suggests a more distant relationship between the two verbs.

He had asked her to marry him before she moved to Topeka.

places the question solidly before the completed action of her move to Topeka.

He asked her to marry him before she moved to Topeka.

places the question in the past and removes any connection between the time of the two verbs, leaving it unclear whether she did in fact ever actually leave.