I think it's telling here that several translations (KJV, ASV, Darby, ERV, WEB at least) will use the word "prepared" rather than "appointed". That is significant. If a great fish is only "appointed" (chosen/selected), you could argue that we are limited to what can be selected from the natural world. If the fish was "prepared", however, then we should expect more supernatural intervention; it could be a species with a single member designed for the explicit purpose of swallowing Jonah. In other words, this opens the door to greater divine intervention.
Science is the study of the Natural Universe, and with the alternate translation the passage here now implies supernatural intervention. Since we have that intervention, as a believer I find the science in this case completely irrelevant... indeed, I might even be disappointed if a simple scientific explanation is found.