Character backgrounds don't write themself so it doesn't work to say that -3 Fort Save is "in character". It's a game mechanic which can just as easily be represented by the low Fort progression her class already has. There is no absolute standard for "how bad" her character's Fort Save needs to be.
Literary heros can be more interesting if they have flaws. Some even have tragic flaws that are very severe. Perhaps the player hopes to set up a situation (her Fort Save) that is a flaw around which roleplaying can be hung. In order to do this the DM will need to cooperate and ignore the rules. The DM's goal with this flaw should be to make it count enough to excite the story but not kill the character randomly due to a bad save and prematurely end the story.
Literary heros can be more interesting if they have flaws. Some even have tragic flaws that are very severe. Perhaps the player hopes to set up a situation (her Fort Save) that is a flaw around which roleplaying can be hung. In order to do this the DM will need to cooperate and ignore the rules. The DM's goal with this flaw should be to make it count enough to excite the story but not kill the character randomly due to a bad save and prematurely end the story.