Please humor me.
Isn't the bolded section simply saying that if the penalty is declined, that would create an end of the run spot for IFP penalty enforcement from the end zone?
Therefore...
An incomplete IFP, accepted or declined, leaves the end of the run at the spot of the illegal pass. Safety in both cases.
A complete IFP (1st pass), accepted, results in a safety.
A complete IFP (1st pass), declined, results of the play.
A complete IFP (2nd pass), accepted, results in a safety.
A complete IFP (2nd pass), declined, results of the play.
Agree?