On #2, indeed, one can provide two different presentations and swap one for another using media queries. That’s a very powerful mechanism. But it leads to verbose code, and I’d argue that it’s better when the mechanism itself scales. Lots of people will use Regions to create multicol layouts, just like the good people at WebPlatform did. I’m happy you see there is a better alternative. What kind of code will Adobe’s tools generate?
On #3, you set the height of the grid to “110vh;”. This makes the grid taller than the screen, which solves some problems, but create others. For example, if you try to reuse that style sheet for a short article, you would end up with white space, no? Is there an implementation that renders your first example as you would like to see it?
On #4, verbosity, you seem to be saying that using Grid or Flexbox will create more compact code? Could you encode the example at hand using your favored technique? I challenge you to write it in three lines :-)
On #5, I don’t think the problem is (nor have I criticized) the design used in WebPlatform’s article. I fear that the problems are much deeper than something that can be fixed by a designer. For example, how would you encode the pullquote example in a way that does not lead to overlapping text or blank areas when the text changes?