Hey, just because I'm paranoid doesn't mean they're not out to get me!
Seriously, though:
Yes, if you have a different pH in the A and the B reservoirs, then you are effectively running a pH gradient superimposed on the salt gradient. Because the column packing itself can "titrate" the mobile phase, non-linear effects are quite possible (this is one of the reasons we tell people to avoid pH gradients if possible). You're dealing with a narrow range, so I wouldn't really expect a problem, but the point to robustness evaluation and validation is to demonstrate that no problem exists.
As long as you are not overloading the system or "challenging" it with an injection of wildly different pH, buffer concentration shouldn't be an issue. However, now that you mention it, it wouldn't hurt to do a couple of extra runs with 40mM and 60 mM just to be sure (again, better to demonstrate that no problem exists).
And yes, the NaCl plays the same role in ion exchange that the organic solvent does in reversed-phase.