The default audio format is FLAC, so that's not the problem (just in case you were wondering). The issue there is that whenever you alter the signal, e.g. slowing down, pitch shifting, etc., you end up with a loss in quality, however large or small. This doesn't happen for volume or EQ as you're only changing the level of the signal, and not the signal itself. So, that slight loss in quality that you're hearing when you save the slowed down song is due to the 10% speed reduction.
I hope that helps explain things.