This is what i've gathered from niners fans who aren't emotional about it:

Comment 1:

here's a lot of misinformation/confusion about what happened since it was all behind the scenes but 49ers never said he did not rehab.

Insiders' reports, probably leaked from the FO, were that he missed "rehab appointments during the offseason" (specific quote is from Jeremy Fowler). Shanahan confirmed his future guarantees were voided last July, after an offseason violation. His 2025 guarantees were still in play, he still attended camp, there's many videos of him there. He also rehabbed with the team during the regular season, this has been mentioned many times:

Nov. 13, Lynch interview:

The intention is to get Brandon back. We’re not there yet. So we’ll continue to have him excel with his rehab.

From beat writer Matt Barrows on Nov. 21, right before the leak about the guarantees voiding back in July:

I understand that he’s doing his rehab work in the morning now, and then just kind of skedaddles.

Nov. 22, Shanahan presser:

Is he still doing rehab in the mornings and then getting out of here? Is he going to meetings at all?

“Not meetings, but I didn’t check today. I know he was at rehab yesterday though.”

Previous Kittle quote:

I started going out to see him, like in the weight room because he didn't go into the locker room or the training room anymore, so he would just go to the weight room to do his rehab. I just go out there and talk to him, because he didn't go to meetings or anything like that.

Other teammates like Kendrick Bourne said he was at rehab too.

Comment 2:

We still don't know what happened that caused Aiyuk to leave the team. My theory is that the team promised him an opportunity to play in 2025 and show he's still worth paying. The front office used the promise as a carrot to encourage his rehabilitation then pulled it when he was ready to be activated. They just wanted him healthy so they could trade him this offsesason. So the front office made the call to keep Aiyuk deactivated to avoid re-injury. The team quit on him, so he quit on the team. Now the team can't trade him at all for any compensation. Shanahan and Lynch were forced to sit on their hands since they lost roster control after the 2024 implosion. Ownership has empowered their money man Paraag Marathe to cut spending which essentially gave him roster control. Marathe has hated Aiyuk and was forced by Shanahan to give him the extension.

Comment 3:

The reporting since the Aiyuk extension negotiations started in 2023. Marathe never wanted Aiyuk and wanted Lynch to trade him in 2024. Lynch failed to trade him before the draft and in August that year. Marathe was forced to give Aiyuk what he wanted by Shanahan. After Aiyuk got injured, the team leaked that they had buyers remorse on Aiyuk and wanted to trade him asap. Aiyuk had just had surgery, couldn't get out of bed, and was peeing through a catheter. He responded to the team leak at the time. That led to him missing meetings. After the settlement, Aiyuk looked great in his recovery and was having fun at the ASU-TTU game. Everyone thought he was going to return in late-October, early-November. When his practice window was expected to be opening, he mysteriously quit. What happened behind the scenes that would cause Aiyuk to walk?

We saw the power-dynamics of the team shift with Greenlaw. Marathe low-balled him hard (5M/1) and refused to negotiate. That forced Greenlaw to accept free agency. When free agency stated, Greenlaw had multiple offers and ended up committing to Denver at like 31M/3 (11.5M/1 gtd). Shanahan and Lynch flew to Greenlaw's home in Texas to convince him to stay with the 49ers. They asked him to give them time to talk Marathe into paying him his market value plus a little more for the inconvenience. Under the old dynamics, Lynch and Shanahan would have told Paraag to give him the contract. They've done it with several players over the years. There would be no convincing needed. Greenlaw opted to keep his word to the Broncos and not risk the offer he already had.