There's a lot of previous work on picking the best compiler flags to tune a program. It doesn't appear that this thesis cites any of that work-- probably because most of the work hasn't been published. JITs by necessity disable many optimizations that aren't always cost-effective, so gaining a few percent improvement by tuning flags isn't surprising.
http://math-atlas.sourceforge.net/atlas_install/node20.html
http://www.vi-hps.org/upload/material/tw13/PTF_CFS.pdf
