Kicking and clock

[Nevadaref]

Originally Posted by billyu2

... so the ball becomes dead when the try is made or when apparent it is missed. In which case, the clock never should have started as well. The whistle in both cases stopped any play from continuing but did not cause the ball to become dead, it already was dead. That seems to be supported quite well by Rule Fundmental #16.

This part is all false and that is why you reach the wrong conclusion.
No rule makes the ball dead in the FT situation. There is no violation or foul. The ball isn't dead until the official sounds the whistle. Everything before then is timed.
For the illegal touch on the throw-in, we have a violation that makes the ball dead and a rule stating that the clock does not start. We also have an NFHS clarification from a few years ago instructing the officials that no time comes off on this infraction.
Two totally different plays which you cannot equate.