Could "applying" jump over the non-essential phrase starting with "which", if it made sense, and modify the clause "Many house builders offer".
the sentence is still nonsense with that interpretation -- obviously, house builders don't pay rent, so it makes no sense to say that house builders will "apply part of the rent" to something -- so it doesn't matter. you're talking about a choice between two nonsense interpretations.
more generally, if a sentence actually required this sort of "jump" to be interpreted correctly, then it would be a very badly written sentence.
GMAC's correct answers are not badly written sentences.