Hi dmitch and welcome here,
I'm adding my comments and you will certainly get more experienced guys, passing by.
Between the Node 304 and FD R4, I don't think there would be much of difference concerning the CPU dissipation.
Using the tower cooler Scythe Kotetsu, the Node 304 should be able to handle it.
But you are planning 3 HDDs, which might do the difference.
It will be easier to suspend them in the R4, than in the Node 304.
After reading around for many months, my preference goes to small factor, because they can handle some power and they seem to have a good airflow path.
Unless in need of 3 PCI cards, 5 HDDs, 2 DVD burners, etc... I don't see the need, today, to use ATX format. (it's my own opinion).
Also, you are not using a graphic card, so why thinking of the R4?
(thanks for the Scythe Kotetsu in your list, I'm going to add to mine. It seems better than HR-02 Macho.