No; it doesn't state that at all - it states that it's an unfair or deceptive practice to increase a price for travel involved scheduled air travel after purchase. Airlines are, as a matter of contract law, able to rescind contracts made under mistake. Section 399.88 was originally interpreted by the DOT as creating strict liability for airlines if they refused to honor mistake fares, but that's different from there being a breach of contract. Breach of contract creates a remedy for the consumer; unfair or deceptive trading practices give rise to civil and administrate penalties by the DOT.
The fact of the matter is that the confrontation with their regulator and the civil penalties involved are in the "greater of two evils" category for the airlines, so there's commercially speaking no way this would ever come to court.
>Is there a single case where any shopkeeper has been held to specific performance?
This has nothing to do with specific performance; that's just one remedy for breach of contract. Why are you suddenly talking about remedies?