Channel A - (2&4) needing to being populated has been an issue since Ryzen 3 series came out, it was an issue if channel b only were used when Ryzen 1800x came out, as well briefly, and didn't matter for Ryzen 2 (A or B). I own 1800x, 2700x and 3900x. This problem if you can call it that is simply fixed by using Channel A as recommended in the motherboard manual. I would not RMA the board (this is repeatable on all of them) and would not worry about this. When you have Channel A populated and then Channel B as well both will work fine, that said you have 2 sticks and as per the manual should be using Channel A.
This in my mind mind is most certainly to be about/around the implementation of the AGESA code, as you suspect, but I would not expect to see addressed because it's really non-issue once you follow recommended use of the slots and to compare to an Intel system, is exactly the same, you cant place the RAM anywhere and expect it to work optimally or correctly.
Hope you find this help 😉