No I don't think you are screwed. In fact it sounds like everything is progressing nicely. Hoping that the asking and offer price as well as any seller concessions are within reasonable market value range & norms and then it's just a waiting game.
Even if you are, the APT is designed to take care of that with a variance.
It would appear that this could not be done in advance, as they didn't know your offer and the FMV as determined by a BPO or Appraisal.
Hang in there.
Good luck and may God bless