B. I think I'll best explain it with an example:
You go to buy a new car, you choose the model you like; at the shop they have a red one... but you'd like a yellow one. So you ask:
«Does this car have to be red?» that is: is it actually possible to have it red only?
And they answer «No, sir, not if you don't want it to be.» that is: no, if you don't want the car to be red you won't have it red.
In general, such a sentence means a thing/situation is not necessarely in a determined way, it's not like that way if you don't want it to be like that. We can analize the sentence this way:
Not: adverb denying a situation/thing previously described
if: particle introducing an hypothesis
you don't want: main hypothesis
it to be: what you don't want (it: subject / to be: verb)
[e.g. If you're unhappy when the weather's cold, you don't want it to be cold.]