Yaourt is just a wrapper to fetch and run build scripts from Arch User Repository. It also automates fetching any subsequent dependencies. However, it plays no part in the actual build process, which is handled by makepkg, itself essentially just a script to parse the build scripts. 

I just successfully built A3 from svn using the same build script both with or without yaourt, and with cwiid-git installed. Just for kicks I uninstalled cwiid and it still builds fine, so something is definitely odd with your system Fero.