THAT does not restrict prepositional phrases.
look at the book on top of the table that fell down.
First of all I didn't understand why you chose this example because the verb following THAT is fell which remains unaffected regardless of whether "on top of the table" is included in the sentence or not.
I'd like to point to some of your own examples
one (of the cars that run on hydrogen) is brown ---> that restricts cars; it's one of the cars that RUN
not one of the cars that RUNS
one (of the cars that run on hydrogen) [in North America] is brown
one (of a large number of communities [on the Great Lakes] that are looking
and so on...
IMO that always restricts the nearest noun regardless of whether the noun is the object of a preposition. Prepositional phrases are parenthetical as far as subject-verb agreement is considered - the true subject of the sentence remains unaffected by an intervening prepo phrase.
Correct me if my understanding is wrong.