Build, release, Run: Applicable to compiled code which is not the case in PHP. So this
point is not something you need to look at.
I don't claim any authority on this 12 factor stuff, but my read of that section is that the author would disagree. It's not just about compiling, it's about managing dependencies both in the small (the snapshot of the code) and in the large (any libraries the code uses).
Imagine you're a new dev and they say, "Okay, this is a custom php app, so...
a) The custom code is really two subprojects, which are in repo A and repo B.
b) You'll need to create a directory layout like so, and then
c) check the code for each subproject out into this subdirectory and this subdirectory.
d) You'll also need these three open source PHP libraries:
version 3.1 of library Foo,
version 2.3 of library Bar, and
version 5.6 of library Bat.
e) download them from their home project sites and unpack them, then copy them into this directory, that directory, and the other directory.
f) then you'll need to set these configurations in the external library,
g) and these configs in our two custom code projects.
h) once that's all done, tar/gzip it all up, upload it up to the QA server and untar it into htdocs.
There's no compiling going in that set of steps, but you can bet there's a lot of building.
Getting all of that set up and working is the build step.
Using tar/gzip to take a snapshot of the working build is the release step.
SCP'ing/unpacking it into the QA server's htdocs directory is the runtime step.
You might say that some of those steps above are unnecessary - the libraries should be deployed at the system level and merely imported. From the 12factors.net site I'd say the author prefers you to import them uniquely and individually for the app. It sidesteps dependency versioning problems at the cost of more disk space (not that anybody cares). There are more hassles in managing all those dependencies as local-to-the-app, but then that's the point of the build/release/runtime scheme.