A few weeks ago, when the Emma Fitzsimmons’ story on Andrew Cuomo’s inability to coexist with Andy Byford first broke in April, the governor took exception to the story. In an appearance on Alan Chartock’s show on WAMC, Cuomo slammed the paper over the story.

“I think they have to sell newspapers. I think that is the way of the world. I think it’s symptomatic of our political system now. You have less public trust in newspapers, in politicians,” he said to Chartock, who just chuckled along with his friend the Governor. Cuomo continued, “There’s a chairman who runs the authority. In this case it’s Pat Foye. And I deal with the chairman. It’s very rare for me to deal with a division head directly.”

To Cuomo, in his public statements at least, Andy Byford, the president of New York City Transit and a globally respected leader in his fielder, was simply a division head, and the Governor of New York couldn’t be bothered with those.

Unsurprisingly, Cuomo’s statement was mere hyperbole. As two MTA sources have since told me, Cuomo regularly talks to actual division heads and even lower-ranking MTA employees. A few days before his appearance on Chartock, Cuomo was on the phone with managers in Transit’s Division of Operations Planning discussing signal timers and speed restrictions, my sources have told me, and in the intervening weeks, Cuomo and his MTA loyalists have continued to involve themselves in Byford’s Save Safe Seconds campaign to speed up the subways and repair faulty signals and recalibrate unnecessarily slow speed limits.

Cuomo, according to a senior MTA official, has tried to implement his own version of moving fast and breaking things, Mark Zuckerberg’s now infamous motto that hasn’t aged too well. The governor, I’ve been told only talks to certain members of the signals team (but not, according to my sources, Byford) and has repeatedly asked why the MTA cannot simply implement a blanket increase in speed and be done with it. The same senior source explained that Transit is implementing the speed increases in a methodical way to ensure passenger safety is paramount, and Cuomo’s approach would be both inefficient and not nearly as safe.

But signals are just one area where the governor has resisted Transit’s — and by extension, Byford’s — authority. As Larry Schwartz and Andy Byford discussed at last week’s MTA Board meeting, the ongoing Grand Central 4/5/6 rehabilitation project is another source of conflict. Byford’s and Schwartz’s exchange was the first the public had heard of any issues with this project, and while it’s a lengthy and messy one, Transit has kept most of the second busiest subway station in NYC open and accessible during a comprehensive rebuild of the station.

Still, as one MTA source relayed to me, a few weeks ago, Melissa DeRosa, a top Cuomo aide, arrived at Grand Central during the height of rush hour and amidst a delay in service on the Lexington Ave. line. She witnessed capacity crowd conditions and promptly raised concerns about the project. Now, Cuomo and his allies on the MTA Board are making noises about the project. One source told me they objected to the replacement of a staircase rather than a repair, and Cuomo’s allies are making noises about removing the project from Transit’s purview and placing it under the auspices of Capital Construction. There’s no real need to do this, and in fact, the complexity of the project and the need to ensure it doesn’t interfere with Lexington Ave. subway service would generally dictate that Transit oversees it. But that’s the nature of the impasse. Cuomo is in charge, and he wants what he wants whether it makes sense.

The back-and-forth between Cuomo and the professional staff at Transit doesn’t end here. One MTA official told me that nearly $1 billion worth of procurement orders are awaiting Cuomo’s signoff and are simply sitting on his desk waiting for action. Since the design-build threshold sits at $25 million, anything over must be design-build or receive a waiver, and Cuomo hasn’t moved on approving these projects. MTA insiders feel this stall tactic by Cuomo is another way for the governor to avoid doling out promised state capital funds to the MTA, on the one hand, while accusing the agency of spending too slowly on the other. Dave Colon explored this issue in a Gotham Gazette piece last month.

It’s one thing for Cuomo to be responsible for the MTA and in charge of the agency (which he is). It’s another for him to be openly or quietly antagonistic toward the men and women he’s tasked with fixing the subway because he either doesn’t like the attention they’ve gotten or worse. This saga came to a head again on Tuesday when WNYC and Gothamist ran a piece questioning the Byford-Cuomo relationship. Despite constant on-the-record denials by Byford to numerous reporters (including me) in recent weeks and one in the piece, WNYC claimed rumors about Byford’s departure were resurfacing. They’re not, but later in the day, Brian Lehrer asked the governor about his relationship with Cuomo, and Reinvent Albany transcribed the exchange.

Cuomo, you’ll note, referred again to the agency presidents as “division heads” and filibustered by talking about the LIRR overtime issues, a problem in which Andy Byford and New York City Transit have no role. After claiming that the MTA “needs to make major reforms” and that the MTA Board will decide Byford’s fate (it won’t; Cuomo will), the governor offered a lukewarm endorsement for Byford and the other agency presidents. The talk on fare hikes to fund Fast Forward, a plan Cuomo should endorse and embrace but won’t, and the claim that he’s on the side of the riders doesn’t ring true at all. Supporting the riders would mean throwing the full weight of his office behind a fully funded Fast Forward plan.

Later in the day, when I asked the governor’s office about his involvement in management and operations decision and his relationship with Byford, his office offered a statement: “The Governor supports Andy Byford; he said it himself on the radio this morning. We’ll leave the conspiracies and gossip to others.”

So as the relationship between the governor and the agency he controls seems to teeter along in some state of unrest — where the governor doesn’t appear to trust the experts he brought in and should trust to get the job done — where does that leave things? Based on the current status quo, Andy Byford isn’t leaving tomorrow or next week. That could change if Cuomo forces him out, and the looming MTA reorganization should be telling one way or another. Will Cuomo try to remove Save Safe Seconds or even the Fast Forward plan from Transit? Could that be a tipping point? We’ll find out soon.

Ultimately, as I wrote in April, I viewed Fitzsimmons’ original story that brought these simmering tensions into the open as a message from Byford’s proponents. Transit allies were trying to get the point across to the governor, in a suitably subtle way, that Cuomo needs Byford to fix the MTA more than Byford needs Cuomo. The governor, if he lets his NYC Transit president do his job, can take credit for being the chief executive of New York State who oversaw the revival of the MTA. Never mind that Cuomo’s neglect got the city into this position; Cuomo’s acceptance of an expert’s plan can get the city out of that position will earn him plaudits. It’s been a rocky few weeks since then, and Cuomo may not be able to step back and let the repair work proceed apace. But if Cuomo pushes out Byford, would anyone qualified and competent even want to take the job next? And where would that leave all of us?

For the sake of the city, this tension should subside, and the MTA funding should flow so repair and modernization work can continue. There’s no real need, other than ego, for any other outcome.