This is wrong. They are merely different. In a nutshell, they all merely contain information on where to get the sources, some dependencies, how to build them and where to install them. Just because a BSD package has a .tar.gz extension does not make it obsolete. All of the the package management functionality is included.
Centralization is a good thing.
The FreeBSD ports tree is trustworthy. The last thing I want is a decentralized ports tree. But you still have freedom even in this. If you don't want to use the official port, go use another. Or build it yourself.