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.
Regarding "that's a Linux-ism" - well yeah? Linux is the main OS this is about. FreeBSD can do what it wants, too.
That's a Linux-ism. Other *nix there is a lot more in /usr/local.
In reality /usr is similar to Windows' System32 directory on most Unicies.
/opt is really the only good place for Java and where I've been putting it for decades (old habits die hard).