I would add the following to your list of causes (of bad/unmaintainable code):

All too frequently, prototype/POC code (never destined to be maintainable in the long-term) is delivered as a fait accomplit - instead of code engineered on the back of the results of the prototype/POC process.

All in all, methinx this (c/w your observations) can all be summarised using the age old maxim/adage:

We can always afford to do it [develop the code] wrong many times, but seemingly we can't afford to do it right first time