Eesave, clock (not timer1 clock source option), and bod settings are in fuses. The rest isn't
The main point of the timer 1 clock source option, by the way (since i suspect thats the one you were wondering about) is so you can use it with tone on the timer 1 hardware pwm pins to generate higher frequency square waves. If taking over timer1, you can set the clock source to the pll in your code too if you so choose.