I'm not 100% sure I'm correct about this, but this was my understanding from the PETS website:
If you don't arrive on an approved route, but your pet still has all microchip/shots/blood tests, the pet will go into quarantine for a couple of DAYS for the parasite testing, and that's it. I checked on this especially because I am afraid to fly and am hoping to take a ship when we move, with the dog. Only planes are approved, though.