OK, you are looking at BOM and you are starting to see why it costs so much...
Actually a lot of time and work was invested into optimizing BOM, and let me assure you that every component is there for a reason:
- 1.8V ref. is used for control DAC's and 1.25V ref. is for AWG DAC. We could use only one, but this would reduce precision for AWG and also increase noise
- there are no wire jumpers on PCB, you are probably looking at heatsink anchor
- 10 nF 0603 capacitors are used on digital inputs (more resistant to ESD), others are used for HF decoupling
- regulators+tvs diodes are located on different input blocks and for different reasons - protection requirements for analog front end are not the same as for ADC or digital inputs
Also, there are no niche and uncommon parts, all parts are available at mouser, except FPGA and heatsink assembly.
If you need to reduce the costs as much as possible (and are willing to make some compromises regarding reliability and performance), then your suggestions could make sense, but even then the difference in price would be small, because the most expensive components are FPGA, ADC, DAC and high speed op-amps.
4 layers??? I'm not saying it's impossible, but it would be extremely difficult to route high speed signals between FX3 <> FPGA <> DDR3 only on 4 layers and almost certainly not without blind/burried vias which costs the same as adding 2 more layers. High speed signals require a solid plane reference and more layers also improves EMI which is important for low noise.