[throwaway7767]

> It's more than what you see in Linux. For example in Linux you have system packages, packages that are in distro repo,

System packages are packages in the distro repo, so those are the same thing.

> and 3rd party repo all sorting configuration and startup scripts in /etc.

Stuff you compile/install from random sources on the internet will place its stuff wherever the upstream decided to place it. The same will happen if you compile that software on FreeBSD. If you're thinking of ports, those are patched to install to the usual places, exactly the same as the packages in the linux distribution repositories.

FreeBSD's base system is very neat and well-organised, and they have an impressive ports tree with ports that integrate fairly well for the most part. But that doesn't extend to third-party software, and it seems silly to include that in a comparison on the linux side.