There's two things here to cover, first, the original question.
Yes, going with a barebones server can still over you just as good of reliability, performance, and capabilities as the big-name, pre-configured systems. The difference comes down to you are doing the legwork of having to test your hardware to ensure it is all working 100% compatible together, and you don't have specialized drivers of firmware made to ensure 100% compatibility for each other. Take for example, a Supermicro barebones system. While they will test a select pool of common RAID controllers, they aren't making custom firmware or driver changes to ensure that these devices are behaving optimally together. With HP, They take their gamut of servers and test them with 100% compatibility with their HP Smart Array RAID controllers and can thus make appropriate firmware and driver revisions to make fixes or optimize operations. Now, that being said, they're still not absolutely perfect either, but they have a focused team of developers and experts basically doing all that work that you otherwise would have to take responsibility for.
The next thing here is the cost of pre-built systems like you metioned with the HP ProLiant servers. Understand there is more than one way to go about purchasing these servers. If you go onto their website and customize a system to have built for you you are going to be paying absolute top dollar for these things. Instead, you can look at pricing a system through a registered HP reseller. As a reseller myself, I can get access to special pricing promotions and discounts that they do not reflect online, so the cost for ordering the same thing would be less than ordering directly through their online web portal. The other option is taking a more "barebones" approach and do it yourself. Many of the HP servers (especially the Smart Buy options) come with a processor and base amount of RAM installed. From there you can install your own hard drives. Again, it is recommended to get HP hard drives because of certified compatibility with the hardware, but yes you can also just get HP compatible Gen8 hard drive caddies and put your own hard drives in there. I'd still HIGHLY recommend going with server-class storage drives if you do use your own hard drives. You can also add more hardware including additional RAM, additional network cards, etc. to the base configuration.