Yes, thinking about it there is a very good reason your method works fine in your case and not in mine - the backing case piece in your system is shallow, so putting in a shelf and screwing the two halves together will be strong; the issue in my design is that the two case halves are more central, so without reinforcement (as I did) there would be lots of flexing potentially. The reason my case halves meet more in the middle is that I wanted a very rounded finish to all the sides, if you try to make that out of one piece you will never get it out of a mold! I also had to plan the angles so one case half was big enough to take the controls and PSone screen mobo, the other half the console and cart / CD drive, and batteries. Took a massive amount of planning, I can tell you!
So yes, I can see completely why your method works for your case; and why it doesn't for mine.
Good work so far, holes look nice and neat, and evenly spaced. Excellent! Should be a nice portable when done.
I know you mentioned about painting in white - however look at your last pic:
...if you spray paint it in a cream or porcelain colour, you will get a slightly lighter version - like:
Colour is very subjective; just mentioning this in case you don't want to use white but use an off-white shade.