If there is no difference between them, then it is unnecessary to change them and this is a case of fixing something not broken.I don't see the difference between freebsd-update and pkgbase. They're both binary updates. To the end user it's all the same.
If you're a developer or keen user, you can always do buldworld/buildkernel/installworld/installkernel. You can even build your own packages, which I've been meaning to do here. If you want legacy style system management you should be building from source. Again, it's all the same.
And no I don't want to compile everything from source every time I want to update a system.