And you compiled using -O2 with scons, too, right? Otherwise this is an unfair comparison. I have numbers close to yours on cygwin, but I cannot convince scons to compile using -O2.
With scons CCFLAGS=-O2, the compile time are about the same. This is not surprising since the core command g++ takes the same amount of time, and ./configure etc are fast here. Anyway, the main motivation of scons was not performance (since g++ etc will not change), rather easy of use and maintainability. I just submitted another patch that allows scons to recognize environment variable and command line flags. spell checker and aikasurus are supposed to work now. Cheers, Bo