Setting Fuse Bits From Arduino IDE?
The Arduinos are shipped without CKDIV8 enabled. 

New chips without bootloader and the chips after chip erase are having CKDIV8 active.

And you can change the clock prescaller in software, but it mess up everything that depends on it. Delays, serial baud rate and USB as well.

However fuse setings are stored in boards.txt definition file. None of the bootloaders would work with default settings. They are usually compiled for 16MHz @5V and  8MHz @3.3V with xtal or resonator. But the custom boards may have much more options.