this particular rule is not confusing or inconsistent to me
Play: 4th and 10 from Team A's 5 yard line. Punt team in. Snap is errant, punter recovers ball in end zone and is surrounded by defense, he scrambles and throws the ball away while still in the end zone. Ball hits the ground uncaught.
No flag down - Team B gets the result of the play - ball on Team A's 5 yard line.
Flag down - Team B has no choice but to take a safety. They cannot choose the original 'result of the play' - because that changed to a safety ONLY because a flag was thrown.
Why is an illegal forward pass (that is incomplete) the ONLY penalty that changes the result of the play?
If a hold, facemask, clip, illegal kick, etc. penalty flag is thrown in the end zone, they can all be declined - and the result of the play doesn't change based on these flags being thrown. Only a flag for an illegal forward pass changes the result of the play.
If the flag is picked up (waved off), then the defense gets what they wanted. Normally, picking up a flag is the same as declining the penalty, but NOT in the case of an illegal forward pass flag.
Now, you can mince words and say that throwing the flag did not cause the play to change - the illegal forward pass did. But that's not true. Only an illegal forward pass that is recognized by the officials WITH A FLAG changes the play. An illegal forward pass unnoticed by officials has the same rules as a regular forward pass.