Nevada, you're so far in left field its funny. You're citing rules that have nothing at all to do with how/when the clock starts. For you "on the court" definition, how about you cite the rule on LGP that inidicates that "on the court" means inbounds? That would be equally relevant.
The clock starting/stopping rules have nothing to do with the rules for what makes a legal throwin.
If the initial contact is also simultaneous with a violation, the correct procedure, if both the throw-in and violation are being covered by the same officials, is for the official to whistle and indicate by keeping the hand raised that the ball has become dead and the clock should not start. It is just plain dumb to chop time in after you see a violation as the ball is already dead. Why would you start the clock after a violation?