Strictly speaking, the RTK rule doesn't mention SKFs.
9-1-4-a says RTK is prohibited "when it is obvious a scrimmage kick may be made" - not whenever Team A snaps from a SKF.
Even if Team A snaps the ball from a SKF, it might cease to be obvious that a kick might be made, if they do something weird - like snap it to the upback. You have to judge whether a kick is still *obviously possible.*
Problem is, one could argue either side. If the upback fakes a forward pass, or tucks the ball and runs sideways, then surely a kick would no longer appear likely. But if the upback instead immediately passes the ball to the punter, and the punter immediately begins his technique, one could make the argument that a kick still appears likely, and that the punter is protected from roughing. But one could just as easily argue that this screams FAKE simply because it's unusual, and thus a kick is no longer likely.
Also, I can think of cases where the converse is true - a kick can appear likely even when an SKF is not present. Suppose a field goal holder lines up less than seven yards back. Technically not an SKF, but an obvious kick possibility nonetheless.