I have a Space Saver with Caps Lock remapped to Ctrl in Linux. I just tried Caps Lock - Shift - S using "xev" and the S does not register an event at all. Honestly, I don't see the utility that such a keystroke would give, and that's coming from a daily Emacs user.
As I said above, CAPS is my only CTRL key. And CTRL+SHIFT+s is quite a common key combo these days, even in Unix land.
And Emacs doesn't use CTRL+shift+letter combos by default since those don't work in terminal emulation.

That's why it's only a nagging problem for me instead of a show stopper.
For giggles, the "real" Ctrl - Shift - S does register an event. It's most likely in the matrix so firmware programming in the board probably doesn't register the 'S,' either. They don't say anything about rewriting anything so wouldn't the matrix still be the same?
I suspect so, but then again, blocking this particular combo is pretty annoying if you use common desktop apps even on Linux.
And I curse the fact that their "Ctrl" keycap to fit into Caps Lock still has a "step" in it. Sheesh. Talk about not knowing the market.
I know. You do get used to it fairly quickly, though.