Thinking about this some more, I think if I were to make an additional suggestion to CDP developers for the build, I would request that the makeprograms.sh script check if PortAudio is found on the system, and ask the user if they want to build the local copy of portaudio if it is not found. This would satisfy two requirements:
1) From the user side, a repo-installed PortAudio for your distribution (e.g., Trisquel, Debian, etc.) will probably be configured to use (and therefore should play nicely) with the audio subsystems used by that distribution (e.g., ALSA, PulseAudio), and over time this library will probably be kept more current by the package maintainer. (On Slackware, you can use a SlackBuild to achieve effectively the same thing, or just compile it yourself.)
2) From the CDP developer side, including the portaudio source will allow these four programs to still reference some of the needed library source files (e.g., pa_ringbuffer.c/.h) for the build, since these don't seem to be included with even the so-called "-dev" packages maintained in many repos.
But as a rule, I would not compile against a local copy of portaudio unless the user really wanted it.