"Before"/"by the time" + past/present perfect

I know that such conjunctions as "by the time" and "before" are followed by present or past simple:

• By the time she arrived, most of the other guests had left.
• By the time we get to the cinema, the film will already have started.
• Before I had a chance to thank him, he’d gone.
• Before I go to work, I jog for at least an hour.

But recently I've come across examples in which past/present perfect is used with "before" and "by the time" clauses:

• By the time she has finished the book, people will have forgotten the incident it's based on.
• By the time he has completed all twelve stages of the Method, the student will have mastered the 5621 most common words of the English language.
• By the time Martha had examined all the medicines, she felt very tired.
• By the time I had finished my lunch, we had to start off again.
• Most of us were in tears by the time he had finished his story.
• Mum phoned before she'd heard the news.
  
• Luckily, we arrived before the plane doors had closed.
  
• Jane went to the zoo before she had finished reading her new book about elephants.
• I saw him before he had seen me.
• You’re interrupting her before she has even spoken.

• Before he had finished his training, he was sacked.

Sometimes past perfect is used twice:

• By the time I'd gotten to the station, my train had already left.
• By the time we'd gotten to the top, we had to come down again.

Personally for me sentences with present/past perfect in "before" and "by the time" clauses don't make sense, because I have got used, that the action before "by the time" and "before" takes place earlier. I'll be grateful, if you explain why perfect tenses are used in the above mentioned examples.