Ok, you are assuming that the node already has the binary somehow. But that's not the case. In the real world we have to ship binaries to users. And this is where you can put your different bootstrapping data for different users.
You can go a lot farther: let users generate a binary distribution of the software to share with each other and hardcode bootstrapping data there obtained from a running network by that user.
> Open source software can be forked
The majority of users are not going to do that, they just don't have the skills. At best there will be a few popular distributions of the same "decentralized" software, with majority of installations controlled by a few entities. At worst - just one centralized entity that controls every installation.