Hi
I've had a close look at your pic and the blanking brackets do seem short but not half height.
It looks like the GPU bracket is soldered to the graphics circuit board so you wont be able to replace it.
I have not seen this before but it looks like a non standard case.Is it an old Dell or HP as they used to use their own non standard components.
If it was me I would buy a cheap modern case.
If you are careful you could cut the bottom of the metal bracket off but you would need a small hacksaw and be careful not to get metal filings onto the board.