In retrospect the only drawback is that a slightly noisy hard disk will sound louder as it echos around a bit more. I went Mystique as it has limited 3D ability in addition to good 2D ability. My machine dual boots to a freeware Unix operating system called Linux, and three buttons are really needed for the X11 windowing system it runs. And those bits are all you need. I could have bought just the top five items and sold my old motherboard, CPU, etc, but I chose to take the chance to sell off all my old bits in one go instead.
People are generally more keen to buy whole systems than just parts.
Shops will always have a markup for building the machine for you. If in any doubt, DON'T attempt self-build on your own. There are elementary precautions to take, like grounding yourself against the danger of static damage, and taking backups of vital data. The front cover popped off under gentle pressure, while the side plates needed two screws to be undone before they dropped out. Different cases have different designs.