Never had it happen on a game myself, but my crew have discussed it when that rule was introduced. We decided to split it into a number of instances.
I would argue that during a regular passing play, a Passer will normally throw even long bombs with a flattish trajectory compared to a punt's trajectory, he doesn't want the pass to come down with snow on it.
Therefore.....
If he throws a overarm pass whose trajectory looks about right for the distance thrown, then not simulating.
If he throws an overarm pass that appears to be deliberately high for the distance it is travelling, then simulating.
If the punter throws it underarm (in a ball relaying style) and high, then I'm certainly thinking he is simulating a scrimmage kick due to the underarm action.
I seem to recall that the reason for adding this rule was that there was a US college team that did have a trick play where the punter would hurl the ball in an underarm style to simulate a kick. They would very often get a DPI or they'd catch the pass - a win/win situation.
Another thing you might consider is the actions of the defender. In what manner is he trying to catch the ball? A punt returner does not catch the ball in the same way as a DB who is thinking "Interception!!", since they know that by rule they have an unimpeded opportunity to catch the kick. The defenders actions can perhaps tell you if he is thinking pass or kick.