Hmm, you're probably right to worry about brass on gold. Nickel plate will solve that (diffusion barrier), but nickel is probably worse than brass for contacts.
Brass is partly passivated by its zinc content (as stainless is passivated by its chrome content), and so is nickel. But nickel's oxide layer is somewhat tough and forms rectifying contacts, so it can be undesirable. I guess the zinc oxide layer is soft enough not to matter under most other applications.
I suppose sending the brass through ENIG is inconvenient or expensive...
I don't like star or split washers on PCB (they chew up the plating), but I'd be happy with cone/wave washers, one per PCB hole I suppose. Tighten the whole thing down and it should sit okay.
I suppose there might be some advantage to using thinner rod, so it's stretchier. The difference between clamping a whole stack versus pinching each board between a pair of nuts is, the sprung length of thread is only a board thickness in the latter case, but includes the board-to-board distance in the former case. So you have some mechanical advantage, having more length of rod versus PCB stack, even though the PCB is that much more flexible.
Tim