Paraag Marathe has been one of the three men in the room on behalf of the 49ers in interviews for a new coach and general manager, along with CEO Jed York and Brian Hampton, the director of football administration and analytics.

Marathe’s title is San Francisco’s chief strategy officer and vice president of football operations. He doesn’t speak publicly about his role in the football department, but he was active in the showcasing of Levi’s Stadium when it was first built in 2014. He led media tours and played a prominent role in the development of various aspects of the billion-dollar venue.

He’s become arguably the second-most important person in San Francisco’s power structure, which hasn’t yielded positive results. The team’s record between the lines, of course, has declined precipitously the last three years after going to three straight conference title games from 2011 to 2013.

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The 49ers this week had two known coaching candidates remove their names from consideration – Patriots offensive coordinator Josh McDaniels and Seahawks offensive line coach Tom Cable – which would have been a considered a disastrous scenario without Kyle Shanahan reportedly willing to fill San Francisco’s job opening.

San Francisco has been one of the NFL’s poster children for dysfunction since Marathe has moved into his prominent role as York’s top lieutenant.

And according to a report from Pro Football Talk, Marathe’s involvement in the power structure is considered an “impediment” to the club in league circles.

Despite the widespread popular belief that the 49ers are currently the most dysfunctional team in football, the thinking in league circles is that, with some tweaks, the G.M. and coaching jobs could be desirable. The impediment to attracting their preferred candidates isn’t owner Jed York; apparently, it’s Chief Strategy Officer and EVP of Football Operations Paraag Marathe. Marathe is, as a practical matter, the Russ Brandon of the 49ers. The only difference is that the 49ers make no secret of Marathe’s influence over the football operations.

Additionally, three general manager candidates either declined an interview request or bowed out of the race. Chiefs director of player personnel Chris Ballard didn’t interview. He was considered the 49ers’ “first, second and third choice” for the job, according to the report. New England’s Nick Caserio, a favorite to pair with McDaniels, didn’t interview either.

Seahawks co-director of player personnel Trent Kirchner withdrew when he found out the 49ers were focusing their search on Shanahan.

Put simply, Marathe has influence, along with the ear of ownership. He’s been there for 16 years, and he has transcended the bubble of accountability in which coaches and General Managers reside. And that’s precisely the kind of dynamic coaches and General Managers try to avoid. Shanahan is embracing it because, as his final package will demonstrate, he leveraged the team’s desperation to his full advantage. Moving forward, however, it’s an elephant in the room that may be serving as an oversized anchor.

Marathe’s involvement has never been fully described by York. He’s known on the outside for his work in analytics and contract negotiations.

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Marathe’s been good at that aspect of his job. The 49ers are among the league leaders in cap space and have no burdensome contracts in 2017 that will impede the team’s massive rebuilding project. Many, if not all, the long-term contracts he’s put together have been team friendly, for what that’s worth.

On the analytics side, the results speak for themselves. The 49ers have been one of the NFL’s worst teams the last two seasons. And there have been rumors swirling since Jim Harbaugh’s departure that coaches have clashed against Marathe’s numbers-based approach.

But one has to wonder how long Marathe’s influence over the football department will last, considering he, along with York, is one of the last men standing over the 49ers’ destruction that happened under his watch.

Shanahan, undoubtedly, will have questions about Marathe’s role, as others likely have during this search. It will be up to York to decide how that power gets delegated.

York’s handling of that situation will dictate how well things go for the next coach and general manager. The smart move for Shanahan would be to ensure he can override Marathe – or the 49ers could be looking at yet another tenuous relationship behind the scenes that bleeds on to the field.