One thing to note: IOhannes and I removed the generated autotools files (configure, m4 stuff, Makefile, Makefile.in) so the source tarball should behave without having to change anything by hand. The configure script was *greatly* updated to facilitate this as well. It should work whether inside the .app or not.
I guess what I don't understand is the need for both a source tarball and a .app which includes all the sources. It should be possible now to build Pd on Mac 10.6 to 10.12 (and soon 10.13) with the same steps.