I noticed no one answered your HDD questions. I would put your parity drives in the expander. I have not come across a reason not to. I bought one of these to hold two SSDs in my SC846:
caddy. You could put your OS/cache drive in there to save a 3.5 bay.
Regarding your question about dummy drives, I cut out a flat piece of cardboard to put into each empty caddy. It made a big difference. I would also suggest you cover the "speed holes" on the outside of the case to maximize the airflow through the drives bays.
Regarding fan replacement, I personally built a 120mm "fan wall" like is shown
here. The only thing I am running into is that the mobo spins them down too much so I need to run with fanspeed set to "heavy IO". I am planning on implementing one of the fan control scripts out there eventually but haven't gotten to it yet.
Finally there are front panel extension cables:
link.
Overall I think you're gonna like that chassis. I'm really glad I went with supermicro.