But I thought BSDs where more monolithic and coherent systems. How is drawing a distinction between base system and non-base system make that true? If anything Linux embodies that philosophy much better. There is no ad-hoc and arbitrary decision between what is part of the base system and what is not. The system as whole is coherently laid out without drawing any base/user distinctions. Daemons are daemons, binaries are binaries, tools are tools, configuration is configuration and they all go in predictable places to become part of the overall system.
Have you read the article? It isn't an ad-hoc distinction. You get the base system with a FreeBSD install. It includes the kernel and everything else that makes it a "FreeBSD system". This is stuff maintained by the BSD team. Everything else is an add-on.
If you blew away /usr/local, you would be left with a pristine (mostly) BSD install.
An analogy is a base windows install and all the associated tools and drivers. Anything else you install on your own is an add-on.
This distinction is hardly arbitrary.
Edit
Seems to me you have a hard time understanding what a "base system" means. This is what the article is trying to explain, and it seems to have gone completely over your head; I can't help with that.
I read the article. The distinction is indeed arbitrary. How much do you need for a base system really? Do you need more than the kernel, network drivers, and the filesystem? Last time I checked FreeBSD came with way more than those things. So someone, somewhere decided to include a whole bunch of other things as part of the base whereas they could just as easily be addon packages. I think FreeBSD includes various compilers and perl by default. Why's that? How is a compiler an essential part of a system? There are no apriori reasons to make certain "addons" part of the base system and others not. Linux does not draw this distinction and reaps the benefits of a more coherent system.
The equivalent of "base system" in linux land is called a distribution and rightfully so. There is nothing basic about a distribution. It is an arbitrary set of choices made by the distribution maintainers and it is sold/advertised as such.
I think the easier way to think about the base system is to look at Mac OS X. Stuff in the /usr are installed along with the Mac OS X system, and when people need other packages (or think some packages that shipped as part of the system is too old), they use their favorite package manager to install it to /usr/local or somewhere outside /usr. This is also the case with FreeBSD base system. The package manager do not manage packages that are installed as a part of the system, only the one installed by the user.
As far as the compiler goes, in my 10.3-RELEASE-p5, I can only see clang 3.4.1. No Python, no Perl, no even Bash. If I happen to need clang 3.8, I can just `pkg install clang38` and it will happily live inside /usr/local separate from the one in /usr/bin (that is probably presented for building the world). This one will be managed by pkg, but the one in /usr/bin will be updated when I upgrade to 11.0-RELEASE (which will ship with 3.8).
Thinking in Linux's terms, is probably like installing Debian stable only the minimum, and use pkgsrc to install the rest of the system to /opt.
You get the base system with a FreeBSD install. It includes the kernel and everything else that makes it a "FreeBSD system". This is stuff maintained by the BSD team. Everything else is an add-on.
This is why I typically find Debian to be a more cohesive system than FreeBSD. If I could run only the base system, or only the base system plus maybe one or two packages, FreeBSD would have a very good story about being developed in a unified, coherent way. But in practice I need a bunch of stuff from ports, and on FreeBSD that much more clearly falls into the "everything else is an add-on" category. There's relatively little integration testing or attempts to make the software in ports do things in a coherent "FreeBSD-style" way; it's a bunch of third-party software delivered mostly as-is. Whereas Debian considers anything in the 'main' Debian repository part of the official release, subject to release-management and integration testing, and ensures it works in a more or less "Debian way". Whether that matters depends on your use case, but for me that makes Debian feel more like a unified system.
I'm thinking mostly about servers here fwiw. On desktop the base/applications distinction works better for me, so I could run "FreeBSD" as a coherent base system and then install some separate applications on top of it, which is all fine. But on servers I prefer the coherent base system to be more "batteries included", including integrated release management of all the major libraries and software packages I'm likely to need. If I deploy on "Debian 8" vs. "FreeBSD 10", for example, the former gives me a much larger set of stable components that work together in a reasonable way, while the latter leaves me to more DIY it outside of the relatively small base system. (Whether this matters of course depends on what you're building.)
If you're having trouble understanding the layout of the filesystem, you only have to man hier: http://www.freebsd.org/cgi/man.cgi?hier(7)