Boy, did state Comptroller Tom DiNapoli miss the point in his audit this week on MTA construction cost overruns.

DiNapoli cited $43 million in over-budget outlays on six NYC Transit projects. The culprits: poor planning work, bureaucratic snafus, contractor workers who get paid even if they don’t show up, etc.

Some goofs were jaw-dropping: The plan to make a subway station accessible for disabled riders, for instance, failed to include lifting the platform for, uh, riders who use wheelchairs. That fix ran $617,000.

NYC Transit boss Andy Byford says the $43 million was just 0.35% of the entire construction budget. Yet it was 5% of the $816 million set aside for the six projects reviewed. At that rate, overruns for the whole $33 billion capital plan would be $1.65 billion — real money even for the MTA.

Worst of all, DiNapoli’s focus on administrative snags ignored the biggest, and most outrageous, drivers of construction outlays. As The New York Times reported in 2017, work to bring the LIRR to Grand Central ran $3.5 billion per mile of track — seven times the world average.

Why? In large part, pricey union-mandated rules, salaries and perks, which fuel billions in excessive costs. Officials like DiNapoli and Gov. Andrew Cuomo don’t want to upset labor by focusing on such issues.

MTA head Pat Foye notes that most of the six projects pre-dated the current leadership. The agency can also now use a “design build” process that can lower costs.

Centralizing control over projects, as the agency’s “transformation” plan calls for, will save money, too, he adds. Some recent work has already come in under budget.

Yet the long-term verdict’s still out. Cuomo needs to be willing to stand up to his construction union pals. And more can be done to boost competition among contractors to keep their prices down.

With the MTA now drawing up another $40 billion construction budget, New Yorkers need to keep their fingers crossed.