I guess I have the advantage of arriving at Hugo via a number of other generators. So actually, I’ve found much of Hugo’s layout to be more obvious than, lets say Jekyll or Hexo.
But you are certainly correct in saying that, for beginners, the many possible layouts and the differences between them are certainly confusing. It is particularly challanging to try and understand why the page that shows the list of categories for example is of Kind taxonomyTerm when, logically, you would expect that to be of Kind taxonomy.
Then the difference between the singular and plural forms is also confusing. Though Hugo is not the only tool that differentiates this way.
Of course, for a Hugo beginner, one of the least consistent and most confusing thing is the seemingly random selection of casing for variable names.
It is certainly interesting to see that @kaushalmodi has done what I suspect most of us have to do and that is to build a test site with lots of debugging. For myself, I’ve had to build a load of partials and shortcodes to find out what is happening and I too have started to build a set of notes about how Hugo puts things together. If you look at my testing site (where you will see that I am trying to migrate from my live blog at it.knightnet.org.uk) https://confident-carson-5eac42.netlify.com, you will see some debug information in the sidebar.