I really like that plexiglass extension for the look it give. Would just have made it thinner however, because it's too fat for my taste, but I understand it was "fit your cooler first"
But who use HDDs nowadays? Especially if you spend that type of money on a case, you can afford to buy a 1 TB Sata 3 SSD without any problem. And if you absolutely want a thick HDD, you can always use double-sided tape.