It seems this is pretty much what goes on all the time in embedded systems shops. It is open to quite a lot of scrutiny, but you can't see what's going on inside the CPU.
Even the FPGA is not fully open. Whenever you design FPGA code you're importing various libraries. Those contain all sorts of hidden logic - even CPUs. For example, the Altera FPGA SDRAM controller has a CPU in it that is not open to scrutiny.
If you really want to see "from scratch" Then look at the work of Chuck Moore. He really built a whole system from the ground up.
First he developed FORTH (a language)... and an OS and desktop.
Then he developed various processors.
When he didn't like the chip development tools, he even developed his own chip design software so he *knows* exactly what goes into the processors he designs.