You're confusing different kinds of "difficult."
Finding the occurrence of the integer "1241482198192234845" somewhere in your computer's memory would be rare, and therefore difficult. But finding such an integer would be a lousy reason to re-route a train track.
The fact that train tracks exist in other places is irrelevant. This about putting a train station in the town of Cotati itself, using an existing rail line. Moving the rail line inside an existing town is hugely expensive -- somewhere between several million dollars and tens of of millions of dollars, depending on the price of Cotati real estate.
Perhaps this tree is important enough that moving the rail line or canceling the station is the right decision. But the fact of the tree's rarity is insufficient justification.