If I recall correctly, ports first appeared but no package (pkg was developed far, far later) were provided. Ports was just hepler for sharing fetching, patching and building efforts within FreeBSD community.
Then, later, packages (at the moment, called packages and maybe in *.tz or *.tgz format) were started providing for convenience, included in CD-ROM image (at the moment), but not in diskettes.
So it was quite natural installing anything built using ports into /usr/local/.
There were NO upgrading tools at the beginning, so ports helped installing new softwares easily, but not much helped for upgrading.
So portupgrade, which is the very first upgrading tool on FreeBSD, was developed to attempting to solve the difficulties on upgrading.
Not 100% sure, but if I recall correctly, NetBSD introduced FreeBSD's ports framework (still far more simple than currently), and FreeBSD already started providing packages. So installing packages into /usr/pkg/ was NOT too strange (strange, though) for NetBSD.
Aftert a while, NetBSD switched frameworks from ports to their original pkgsrc, and now it is.