Project 2025 and Agenda 47 are both trying to do different things. They're not in competition and they don't really contradict each other in principle.
Project 2025 is primarily a database of vetted candidates that Trump could use to appoint new people once he redesignates federal bureaucrats into Schedule F employees, as he's promised to do. This would give President Trump the ability to fire 20,000 "deep state" bureaucrats that tried to obstruct his agenda the last time.
Project 2025 was created largely by former members of the Trump admin to give Trump supporters the education they'd need to fill these newly available roles. It also comes with a 900 page book full of suggestions for the next Trump administration. But they never claimed to represent Trump's official campaign agenda. It's basically like if you got together with your neighbors and came up with a list of things you'd like Trump to do as President. It's not actually meant to challenge him or represent his official policy.
Agenda 47 is Trump's official campaign agenda. It's the package of proposals officially endorsed by President Trump and his campaign.
The media is attacking Project 2025 hard and I suspect President Trump doesn't see the worth in defending it at this point when it brings so much negative attention. The media is overwhelmingly liberal and it opposes Project 2025 for the same reasons it opposed President Trump throughout his political career. I think disavowing it is more strategic than ideological. It allows Trump to portray himself as a "moderate" and win more independent voters.
The Trump campaign has also recently paid a lot of MAGA influencers to disavow Project 2025 and promote Agenda 47, portraying them (unfairly I think) as competition rather than two separate things that could theoretically work together. The two aren't separate, competing proposals though. Everyone involved with Project 2025 supports Trump and understands that he gets the final say. Project 2025 was created to help the next Trump administration, not counteract it. It's an unfortunate casualty of the biased media environment that Trump now has to court.
And if it was created largely by former members of the Trump admin? Many of them were closet RINO's and working against Trump, so why should they be listened to? Leave him alone and let him choose his own people.
Project 2025 was created to address that very problem.