Here's the issue for the bottom. If the HD does not have the bottom plate, a flat block on the bottom will contact a series of contacts (at least on the seagate 40GB right next to me) and possibly cause problems, or it will be a couple millimetres from contact with the motor. Now, while the heat may be produced on the bottom, you'll note that the sides get nearly as warm. The sides don't have contacts, so attaching the waterblock there is safe, will make good contact, and will probably do a good enough job (any problems with HD stability from heat?)
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