Hi Ricky,
It's a while ago that I made a 'app' from Pd that way. Probably, you can pick all the binaries and abstractions you need from within the Pd-extended folder if they didn't come with the 'app'.
I also made an 'app' from Vanilla Pd, and it does not even have the 'make app' option. It's a matter of copying all the stuff you need into the 'extra' folder, setting startup items and flags, setting the new name in Info.plist etcetera. And coolest of all, you can make a new icon for your app with Icon Composer...
With Vanilla Pd, the app is quite a bit more compact. Ah, there's one complication with the so called standalones: it must have it's own preferences file. Do not set preferences from the app's menu - or they will be written into the shared preferences file for all Pd-extended installations on your computer. Make a preference file by hand instead, using X-code's Property List Editor and store it in the app's Contents folder.
Katja