It's got a mass of relatively expensive hardware components that have (almost( never been included in a laptop form factor and certainly not together. Novena can replace quite a few expensive discrete tools and do it in something that can be comfortable carried around and modded. What you're asking is basically why a full shop with a CNC mill installed in a large truck is so much more expensive than a nice pickup when the latter can go much faster and is a lot more comfortable. They share a category and vaguely similar basic shapes, but they're not really the same thing and you don't use them as if they are. Is that a helpful analogy?
Field replacement for oscilloscopes & some logic analyzer uses. Software Defined Radio host (the expansion card is in development). Hardware reverse engineering including bus-sniffing something while it's running. Feeding signals into stopped or running hardware to plant new firmware in it. Sniffing crypto keys from running hardware - Bunnie Huang is one of the core Novena people and he was the one who used an FPGA to sniff the Xbox crypto keys to allow Xbox Linux to boot. Keyboard & LCD can be switched at will by a user. The FPGA can be programmed to do many things faster than a general-purpose CPU and can do fast/wide data capture a CPU simply can't keep up with. The expansion slots have room and interface capability that can support a lot of potential new hardware including home-built modules. The list goes on from there, but my fingers are going on from there.
The CPU & graphics are almost more of a programmer convenience than a fundamental selling point. You've got to have them, but they're there to control other things and do some basic number crunching.
Any time I design a laptop into, say, a robotics system, I have to buy at least a dozen spares and store them away, because five years later when the laptop dies and a $500,000 machine that generates $1,000 per hour in profits goes down, that model of laptop will no longer be available. With open-hardware like Novena, I have a good chance of being able to make a new one that is compatible five years down the road, and can get by with two spares in storage.