The fight between Mayor Kirk Caldwell and the City Council over SamKoo Hawaii’s 513-unit condominium near the Ala Moana Center rail terminus again points up the the chaos that bedevils rail.

Over Caldwell’s objections, the Council approved the 43-story project as a transit-oriented development, giving zoning exemptions, height and density variances and fee waivers worth more than $10 million.

The mayor wanted more time to negotiate with the developer to include its project in a transit center that will be essential to getting rail passengers from Ala Moana to the University of Hawaii, Waikiki and other points east.

It’s hard to say which is more alarming: that 12 years into planning rail we still don’t know where a mission-critical transit hub will go, or that transit-oriented developers can collect their bounty of fee waivers and variances without having to actually coordinate with the transit system.

The Council’s decision may preclude the last workable route for getting rail from Ala Moana to the University of Hawaii, supposedly the train’s ultimate destination.

It’s another example of how the city’s winging it has run up rail costs from $5.2 billion to $9 billion-plus — and it’s not the only major issue still hanging 12 years into the planning and nearly halfway into the construction.

The city has no idea how it’ll pay some $140 million a year in operating subsidies and is sketchy about dealing with expected sea-level rise that could flood seven of the eight final stations barely two decades years after the full system opens, according to its own Climate Change Commission.

As construction approaches Middle Street, we’re at our last chance to pause, resolve these critical issues and finish the troublesome project right instead of persisting with costly improvisation.

We know far more about sea-level rise than when the route was planned 12 years ago and would be foolish not to apply the latest information to the rail plan.

State House Finance Chairwoman Sylvia Luke, who oversaw $3 billion in legislative bailouts for rail since 2015, told the Honolulu Authority for Rapid Transportation last month what many think: The only real solution to future high-tide flooding is moving the route inland.

This would mean resurrecting an original option to run the final leg of rail along the King-Beretania corridor to the University of Hawaii instead of the Nimitz Highway corridor to Ala Moana Center.

Luke said the change would raise short-term construction costs, but could save more in the long-term buildout to UH.

The city dismissed the idea, but hasn’t heard the end of it; Luke said the House plans hearings on sea-level rise and will require the city, by subpoena if necessary, to finally be forthright about the flooding threat to rail.

Reach David Shapiro at volcanicash@gmail.com.