I read that and thought to myself "So what? " They're all perfectly readable and consider that an excellent example of bikeshedding.

Further up it suggests "Don’t use several empty lines in a row." I put two lines between every method and it makes a language where every block ends with `end` far more easy to grok just from the shape.

It seems I won't be using all of their suggestions.

In my book the third example is also bad, only the simple indentation is good.

None of your examples pose a fundamental problem for tab-indentation; here's the basics how it should (always) be done, and works, and never breaks anything regardless of the width of the tab character as long as you don't break the gist (which is the hard part, especially with editors which sometimes work against you):

  def send_mail(source)
  TABMailer.deliver(to: 'bob@example.com',
  TAB               from: 'us@example.com',
  TAB               subject: 'Important message',
  TAB               body: source.text)
  end

Here, TAB has a width of three but of course the alignment would stay put even if it were wider or narrower.