Are you sure the AUDIO=runtime flags are being set during the build?
In line 30 of src/Makefile, espeak sets AUDIO=portaudio. This could be overriding the AUDIO setting like CXXFLAGS were being overrided in bug #707925.
If AUDIO=runtime is built correctly, both wave.cpp and wave_pulse.cpp should be compiled and -DUSE_PULSEAUDIO -DUSE_PORTAUDIO should be passed to the compiler (see lines 37-39).
The code in src/wave.cpp is doing the right thing, as I have built eSpeak with AUDIO=runtime (not through this package) and it does not invoke Pa_Initialize, but does invoke pa_simple_new.