The problem starts when you need to use 2 or 3 holes - like in my bucket wheel excavator for TC22. I had to pair these elements which was a bit of pain, but still possible.
In my 42120 (I bought it on March last year) axle holes orientation was correct. I saw this discussion before and one user said that the problem already looks resolved, which is why I was surprised with my order from this year. So you are right, I was just unlucky.