At the risk of veering further off topic, we some times use an arduino or the like to bang out a quick proof, but you're right in that these never make it into anything real.
The idea is that the microcontrollers that these platforms are based on have a many peripherals that can do most of the common operations I need to do in hardware without the need for an FPGA. For most of my applications a 100 MHz 32-bit CPU is serious horsepower when I have the heavy lifting offloaded to the peripheral hardware. When the on board peripherals are insufficient there's literally over a dozen communication options, often with several instances of each never mind the ability to tap right into the system bus on the more sophisticated µC architectures. Need to upgrade up the ADC? Fine, that's a $15 IC that will tap into the SPI bus. Easy. Repeat for a few other obscure needs that the built-in stuff can't handle and when all is said in done I have a board that does exactly what we need and costs maybe $200-$500 per unit at volumes of 10-25.
While I have no problem building a single $5,000 NI platform to test something, scaling the volume is sometimes a hard sell. What happens when we need to make 5 more to move from proof to concept? Then 25 more to ship around the world for collaborators to test and bang on for a bit? It's hard to sweep numbers like that under the rug for lower visibility projects, but even for the high ones where it could fly, how do I fit one of those NI boxes in my widget that's supposed to be smaller than any of the NI chassis (except the SOM, obviously)