And I think you're looking at things from the wrong angle.
First, the company policy is absolutely, positively, 100% legal.
Second, even though you are on FMLA, under the law you can be required to follow company policy UNLESS it is not possible to do so.
Third, the company does not have to void their policy; they only have to ON SOME SPECIFIC SITUATIONS exempt you from it.
Fourth, if they are saying that you never have to do anything more than call in same day, that's fine. But LEGALLY they can require you to follow company policy, and discipline you when you do not, UNLESS the circumstances of THAT PARTICULAR MIGRAINE make it impossible for you to do so THAT TIME. They do not HAVE to give you a free pass to violate policy each and every time. They MAY exempt you from following policy at all - They are not REQUIRED to do so except when it is NOT POSSIBLE for you to follow it.

