Since Linux has no concept of a base system, it's a stand-alone kernel with a hodgepodge of crap around it - this distinction makes no sense on Linux.
/opt is generally for software distros for which you don't have source; only binaries. Like commercial software packages. More common on Real UNIX(R) because most Linux users outside enterprise aren't running commercial software. You're putting your $500k EDA software under /opt.
The ports tree will still be very different from base, but I feel this may erode some of the difference between FreeBSD and a typical Linux distro in terms of user experience, with respect to base vs ports. You'll update both with pkg.