Although there are a range of flexibility benefits with an NVR being built into part of a PC assembly, standalone units are generally built on a embedded Linux core and as mentioned, there is a trade off. Using third party software is generally not an option.
The white paper titled '
Benefits of Embedded Network Video Recorders (NVRs) over PC-based NVRs' explains some fundamentals very well and compares the options excellently.
To summarize, the benefits an embedded NVR offers – reliability, stability, ease of use and more – allows for maximizing the value of already owned devices. Moreover, with all the components embedded into one box, it occupies small space and can be perfectly disguised in any location. This makes the embedded approach more suitable to be installed in any spot, even hard-to-reach locations and prohibiting unauthorized intruders access to sensitive video footage.
I recommend reading the full paper here:
http://www.hikvision.com/en/us/Press-Release-details.asp?id=1883