It certainly could. Din created the land and nature. without her everything could change, forest over time become swamps, sea levels rise ect...Aonuma stated that it's a parallel world. Given the fact that the Skull Kid originally lived in Termina and came to Hyrule tells me that they are two entirely different, yet similar, kingdoms. If it was an alternate reality of Hyrule, but where the population abandoned the goddesses, then why is the geography so different? Abandoning the goddesses wouldn't change the actual physical layout of the land.