Yeah... those pics are worst-case scenario when it comes to components. I plan on just putting a SSD and a HDD in whatever optical bay makes it easiest to route cables coming out of the PSU. Then I can throw another HDD in that bottom removable spot. Pop the 4-drive bay out and cable management...
I mean you can and will short out your mobo. Use the stand-offs.
And those "hooks" should be bent inward but should contact the sides of your each cover for the I/O ports. It is to make sure everything is grounded so you don't fry any peripherals or the motherboard.