Your right the card does hang down quite a bit, but the triple slot cooler is very and I think the cables are also pushing down a bit because they were initially routed to the first 16x (next to the sound card) which is now blocked due to de right angled sata cable.
The built in support stuff was connected to the logicboard and was damaged when I removed it, also since my mainboard sits now further down (where the PSU was) it would have been al lot of work to modify it.