Your post rings true. On the contrary the linked article was written by an undergrad student having some introduction to research, for a short time (a year) with a supporting supervisor and network so of course his list is naive and idealistic. In reality research and methodology etc. doesn't matter much, it's baseline skill. 70-80% of a PhD come done to social things like relationship with advisor, ability to write papers that will be accepted for publication even if they're bullshit.