Using Introjucer built from the "3.1.1" tag. I haven't tried current head of master because as far as I can see nothing of relevance has changed in the Introjucer between this tag and the latest commit.
I have an audio plugin that builds in Xcode for both VST and AU. Unchecking the "Build VST" box and saving the project removes the post-build script that copies the compiled plugin into the system plugin folder. I can't see any reason why this script wouldn't be useful for AU only plugins.
I'd imagine this is quite an easy fix, so if you tell me this isn't desired behaviour I'd be happy to jump in and try to submit a PR.
Edit: Forgot to mention this is on Yosemite with Xcode 6.1.1