I can't tell you about Pin Popper but these games use the same logic as the real thing. So for example, if a ball hits switch 37 in the real game, there is a switch 37 in the vp code of the table too.
I can tell you as a former operator, these games go through their cycle at power up. They will say IRL "Pinball Missing" while it's checking for the balls. That check usually takes about 10 seconds or so. Then it should go into it's normal attract mode.