If it works like linux ...
Unfortunately, it doesn't. Applications launched from the graphical desktop interface don't inherit the user's environment on Mac OS X; the .profile configuration file works exclusively for pure shell sessions (including ssh sessions).
You must define the required environment variables within PixInsight. It is actually very easy because PixInsight provides an internal 'export' command. A script similar to the following will do the trick:
export PCLDIR=$HOME/PCL
export PCLBINDIR32=$PCLDIR/dist/PixInsight32.app/Contents/MacOS
export PCLBINDIR64=$PCLDIR/dist/PixInsight64.app/Contents/MacOS
export PCLBINDIR=$PCLBINDIR64
export PCLLIBDIR32=$PCLDIR/lib/x86
export PCLLIBDIR64=$PCLDIR/lib/x86_64
export PCLLIBDIR=$PCLLIBDIR64
export PCLINCDIR=$PCLDIR/include
export PCLSRCDIR=$PCLDIR/src
These commands assume that you have your PCL distribution on your home folder, and copies of the PixInsight Core application (both 32-bit and 64-bit versions) on a dist subfolder. You must change the variable values to adapt them to your particular conditions.
You must execute the above commands on PixInsight's Processing Console. You can do that in several ways: manually (tedious), adding the above commands to your startup.scp script, or simply writing them to a new .scp file (for example, setenv.scp on your home folder) and invoking it with:
run $HOME/setenv.scp
The latter is the recommended option. Once you have defined the required environment variables, MakefileGenerator will run without problems.
Let me know how it goes.