Had already been + adj + when....

Over as used here is an adverb. The problem is not the adverb ('over') but rather the verb "had been". We use the simple past 'was' when talking about completed actions. The class was already over when I got there. The dog was dead when it was pulled out of the river.

We use the past perfect continuous (e.g. 'had been over') to show that something started in the past and continued up until another time in the past - the class had been over for thirty minutes when I arrived.

If the sentence in question meant to show that the class started in the past and continued up until another time in the past, then the verb "had been" would appropriate and not problematic. I see nothing wrong with that sentence in that regard.

No, because it is the fact of the class being over that he found when he arrived. If something is over it is over for ever, that is, it is over now, and will still be over in the future. Being over never 'completes'. No native speaker would use that sentence without an expression of time such as I showed.

You would not say by the time he arrived at the hospital his grandmother had been dead (another permanent state). You could say by the time he arrived at the hospital his grandmother had been dead for ten minutes, because being dead for ten minutes in the past is a completed thing.

Excellent. Everything you mentioned had already occurred * * to me. I just wasn't able to formulate it as precisely as your explanation. Thank you!

That explanation of the past perfect continuous is limited, and your assertion that "no native speaker would use that sentence without an expression of time" is an unfounded assumption.

According to englishpage.com, "if you do not include a duration such as 'for five minutes,' 'for two weeks' or 'since Friday,' many English speakers choose to use the Past Continuous rather than the Past Perfect Continuous." It doesn't state that no native speaker would use it otherwise. It goes on to state that "past continuous emphasizes interrupted actions, whereas past perfect continuous emphasizes a duration of time before something in the past," which is exactly what the sentence in question is stating.

Englishgrammarsecrets.com states that we use the past perfect continuous "to say what had been happening before something else happened and includes an example without a duration of time," e.g "it had been snowing for a while before we left."

The class being over was not completed. The class having been declared over by the teacher was, of course.

"For a while" is an (indefinite) duration of time.

You're right.

All of the examples I've found use the past perfect continuous with present continuous verb tense -ing.