I would assume it meant that it made things slower, after all this was a hand-tuned numerical core. Optimizations is for what a human did not already optimize.
If by this you mean higher levels of optimization made things slower, than I must disagree. He says "Compiling C code with optimizations enabled is obviously a good idea" he would have mentioned it here if -O2 or -O3 were slower. Also, the optimizer doesn't optimize hand written assembly. Only c code.
What I actually think happened is he didn't understand that there were higher optimization levels that -O1, which gives his code an advantage when compared to the c code implementation.
