That's the way it's built, stock, your psu should sit on top of it and screw into the standardized bracket. I'm sure someone with an HAF will be in here to confirm but your psu will be fine with the case.
When painting the prep is critical, if you did a good job with the sanding and it's peeling chances are you used the wrong type of primer, you need to match your primer to the type of material you are painting. For bare metal a self-etching primer (acidic component) will adhere into the metal. This will give a better grip so to speak so chipping is less likely, and shouldn't happen.
Here is what I use for a standard black paint job, bought from local NAPA auto supply:
From left to right:
1) self etching primer (spray can)
2) flat black (spray can)
3-5) 3 part paint mix of catalyst, reducer and pigment (Mercedes gloss black)
I can get one mid-tower case done with what you see there, the reducer and catalyst will last years. Flat black interior and gloss black exterior.