Prebuilts are universally loathed as gaming computers partially due to the reason you listed. Some parts are proprietary, and can't be replaced by the end user. The quality of parts are usually questionable, as Original End Manufacturers just make it pass a benchmark test and not quality control and ship it off. They also usually charge more for replacement parts versus something you can just get off the market. There's also bloatware that they load up and it's annoying to get rid of.
Building one allows you to set your own budget, and the experience in putting one together helps if you want to modify your computer on the fly. However, they come with absolutely no software, so you're going to have to pay for an operating system, as well as download whatever freeware, including security and office suites, off the Internet. Support will also be limited to the individual parts and not the whole computer.
I've read the specs as well. Not too awfully shabby, but there's a few things I want to ask:
- How much storage capacity do you need, anyway? You can probably knock it down 500GB to a TB, and cross the solid-state drive off the list, since you won't care for boot times until later down the road.
- Do you plan to overclock? If no, get the i5-3450/3470, and the Hyper 212 Evo as your cooler instead of the NH-D14.
- GTX 560 SE is pretty old. You planning to play anything other than World of Warcraft? If so, get one, replace it with a GTX 560 Ti. 560 SE's OEM. If not, if you can burn a little more cash, get a 660 Ti.
- If you do plan to build, do you need to use an OS license more than once? If not, get the OEM disk.
Anyway, this neat little guide might be able to help a bit more. Unfortunately, it's also in USD, so there's that. Compare prices on your end, an OEM system versus a built one, and what it'll do for you on the long run.
On #SPP as: Revan, Artorias