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 Linux base system is managed by the package manager, leaving local for the sysadmin to `make install` into
There is no such thing as a Linux base system.
Separate components, separate people.
Hence the term Ganoo plus Leenox...
In most distributions yes, there is Linux and then there is userspace on top of it. What you call "base system" is actually part of userspace, which has nothing to do with Linux itself.