Atwood is fairly open with her metaphors, and pretty versatile about the way she uses them.
It’d be hard to say that the whole novel is a metaphor, and yet in certain ways it is: Feminism, religious extremism, government control, gender bias, it’s all here. Even the dress code of the handmaid’s is metaphorical; red, similiar to a nun’s habit in shape and form. Oddly enough, after half a book of calling the headress "wings," Attwood finally mentions the word "wimple" which historians and Catholics will immediately recognize.
There are nuances in metaphor, but there are ones made obvious by Attwood, as in the protagonist’s recalling a TV program about the mistress of one of Hitler’s SS commanders. This is immediately following Offred’s puzzling secret meeting with the Commander, wherein he asked her to play Scrabble with him and sought only that and a good night kiss from her. Both actions, and the meeting itself, would be forbidden. The mistress, she remembers, insisted that her lover was not a monster. But what Offred remembers the strongest:
Nobody asked her whether or not she had loved him.
What I remember now, most of all, is the make-up. (p. 146)
The make-up: Colored over, dressed up, hiding the truth. Here is where Atwood becomes more subtle with her use of metaphor, and where it is up to the reader–and Atwood doesn’t really like to let the reader misconstrue her meaning–to consider the possibilities.