I feel that Giro crash fest explains it pretty well.
How does a crash that happened almost a year ago explain his lack of punch and overall lower level in Tirreno and Milano-Torino?
His level hasn't dropped exaggeratedly so there is no reason to believe there is anything wrong with him in terms of still recovering from that Giro crash (no injuries that we know of) or any recent or past illness. Most rational conclusion is that his current shape has absolutely nothing to do with whatever happened last year.
In my opinion both he and the team believed in the "being better in the 2nd GT" pattern, after all that's what he was used to, regardless of how well (or badly) he ended the first GT. We all know how he's crashed out of Tours and went on to win Vueltas despite imperfect preparation, so what changed last year? I don't think that the Giro crashes were worse or particularly disruptive, I believe that the Giro - Tour combo was the issue and that he would've struggled even if he finished the Giro in one piece. That was the unknown (and risky!) variable in the 2 GTs per season pattern, and the crashes made it even more obvious.
But again, what does it have to do with the last half of his '25 season and the start of this year's? He went to altitude and underperformed twice, when he used to come down from the volcano flying.
So these two patterns (2 GTs a season with the second one being his best, achieving his top level after altitude training) have been disrupted despite them believing and expecting that they were going to work. To me the only explanation is that his body, due to age and/or all the injuries and recoveries, has had enough and does not respond as expected.