You can set the fuses to a value that "bricks" the microcontroller. The most common way to do this is to set the fuses to use an external clock source when there is no external clock source. The solution is to connect an external clock long enough to set the fuses back to using the internal oscillator.You can also set the fuses so that the reset pin becomes an IO pin (RSTDISBL). The solution to that is to connect a high voltage programmer to the chip and set the fuses so that the reset pin becomes a reset pin again.I would recommend just using the Arduino IDE to burn bootloaders. The board definitions have ideal fuse settings, which are automatically programmed during the Burn Bootloader process. If you want a good level of control over the fuse settings, MiniCore provides this via custom Tools menu items:https://github.com/MCUdude/MiniCore
I'm not aware of any way that reading the fuses could cause a problem.