Why 49ers honeymoon isn’t over between Shanahan and Lynch, yet

SANTA CLARA — Friction between a 49ers coach and general manager is nothing new, and it’s imploded many a pairing. Such juicy news typically comes as a shock, then with subsequent denials.

Now let’s put the 49ers’ sordid history aside and get back to the present.

It’s highly doubtful Kyle Shanahan and John Lynch are on the rocks only two years into a marriage that Shanahan himself arranged.

On Tuesday, Bleacher Report’s NFL draft analyst Matt Miller launched the first flare about 49ers discord since the regime took shape in 2017. Bogged down midway through Miller’s draft summary, he cited anonymous team sources claiming Shanahan does not trust Lynch’s decision making and they don’t share the same vision.

Shanahan quickly tried extinguishing all that, telling NBC Sports Bay Area the report is “complete (B.S.).” Lynch is expected to weigh in similarly Friday in a radio hit.

Shanahan hand-picked Lynch for the GM role. That little fact makes it difficult to interpret Miller’s Tuesday claim of Shanahan “looking for his own personnel man to run the draft and free agency.” Didn’t he do that already?

Four years remain on their contracts, and 49ers ownership hasn’t stopped raving about their chemistry and the foundation they’re building, even after 6-10 and 4-12 seasons.

They shared a stage throughout last week’s draft without rolling their eyes, without clipped responses, without any sign of indignation. Were they 8-for-8 in agreement on their picks? Maybe, maybe not. Move on or move out.

They looked as harmonious as always. Like their smiling chats on the field before practices the past two years. Like when they chilled in a hotel lobby late at night during February’s scouting combine. Like they do at so many team functions, community events and social gatherings.

They indeed mix with business with pleasure.

Does it look the same behind closed doors? What do any of us really know about our neighbors when they’re not mowing the lawn or making small talk while picking newspapers off their driveway?

Miller’s report cited anonymous sources in the 49ers scouting and coaching staffs. Perhaps only Lynch and Shanahan know the whole truth. Players will sense it and respond with how they play, whether this regime is worth battling for and defending.

All coach and GM partnerships eventually end. How fast and why typically depends on the win/loss column, and the 49ers need to vastly improve this year, no doubt.

Look at perennial playoff contenders – the New England Patriots, the Pittsburgh Steelers, the New Orleans Saints, the Seattle Seahawks – and you’ll see long-term pairings of a coach and GM.

Relationships unravel when the winning stops, or never starts.

Egos clash. Feelings get hurt. Then come rumors, leaks, secrets, white lies, noise. It all adds up until … kaboom.

The 49ers can teach a college class in that. To wit:

— Steve Mariucci and Terry Donahue playfully hugged it out in front of the media on the practice field amid reports of discord. But Mariucci eventually got fired – “There was too much noise,” owner John York said then — and Donahue got the boot two years later.

— Remember when Mike Nolan had the “trigger” over Scot McCloughan over personnel decisions? McCloughan seized it three years later and Nolan was gone by midseason 2008.

— Jim Harbaugh and Trent Baalke denied any rift after three straight runs to the NFC Championship Game. Harbaugh was gone a year later, and Baalke burned through two more coaches before he left, too.

Shanahan and Lynch can break that trend or continue it. We will know for sure in the next year or two. But not yet.