It’s just that most (if not all) build system in the source code package would assume some level of FHS compliance.
For example, they would install:
executables under /bin /usr/bin
libraries under /lib or /usr/lib
sysconfigs under /etc
manpages under /usr/share/man
and so on…
These build systems would include options to change these, but you’d then have to change all these values to adapt to nix structure. While it’s all been done by the nix package maintainers, you’d have to do all that if you’re to come up with a new package.
In the FHS compliant distros, the maintainers wouldn’t need to change anything since these values are already set to the values they want (there are actually minor details they’d change, but that’s another topic).