San Francisco drafted McGlinchey (6-8, 310) out of Notre Dame with the No. 9 overall pick in 2018. The offensive lineman expressed a desire to remain with the 49ers but understands the business side of the NFL.
"Obviously, it's something that was expected," McGlinchey said on KNBR last week. "It's something that the writing was kind of on the wall a little bit, in that regard. [General manager] John [Lynch] and [head coach] Kyle [Shanahan] both had conversations with me before I left the building about that, and it was something that we all kind of expected, but it's definitely a tough deal.
"We have a lot of great players in the 49ers organization, which is why we've been so good for the last five years, and it makes it really hard to afford everybody. And we have a Hall of Fame and probably one of the greatest to play the tackle position (Trent Williams) on our team already, and it's hard to imagine them paying top dollar for both."
Lynch expected McGlinchey to be highly coveted in free agency, pricing him out of San Francisco's future plans. He hopes the team has insulated itself sufficiently enough to withstand the loss.
"You have to have the patience and vision to allow some of these guys to walk," Lynch said. "Get some comp picks as a result, play that game. It took Kyle and I a little while to figure that one out. But you've got to understand you can't just go full throttle, and you get some rewards if you have a little more discipline. It's never easy, but it is necessary."
McGlinchey, 28, has 69 game appearances, all starts, through his five NFL seasons.
"I'm extremely fond of the time that I've had there," McGlinchey said. "I think the Niners are a first-class organization all the way. I believe that the York family is one of the top ownership groups in football. I'm very thankful to have had the opportunity to play for them and thankful [to] John and Kyle for giving me my shot in the league.
"The Niners have one of the best support staff I've ever been around, people that are like family to me now, and a lot of my best friends are in the locker room. And on top of it, I wouldn't have met my wife if I didn't get drafted by the 49ers. So it all worked out in a great way. It's been my home for the last five years, and the Bay will remain my home, but I might have to take a six-month hiatus each year [in the future].
"I couldn't be prouder of the time that I've spent with the 49ers and the work that we've put in, the journey that we've been on. We had our hearts broken a number of times and just kept battling and kept coming back. And I think that speaks to the character of who we were and the guys that are in that locker room and the guys that have been the core guys for the last five or six years. And I'm happy and proud to have been one of them."
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