If both monitors have similar configuration (DPI, refresh rate) it is fine (Xrandr fixed many of the issues that X previously had). If the monitors have different configurations it isn't, but this problem will reflect even on the desktop and I am sure that nobody will report a problem that they have on desktop as a "game bug".
> full-screen programs
X doesn't have a concept of full-screen, but anyway, it mostly works fine if you grab the root window (that of course you shouldn't write code manually to do this, your game engine probably will do it for you automatically).
> low-latency input
X latency is fine for most games, and in many cases you will not use X to handle input anyway. Also, if your game really needs low-latency (only a minorit of genres do), you can bypass X.
Anyway, I was not referring to specific X or PulseAudio problems that you will if you put things on container or not. I am just saying that even if steam-runtime doesn't built-in those libraries it is not much of a problem since those APIs are stable.