Burn bootloader to 32u4 fails

This has been an issue for a few years now. The Arduino IDE (currently using 2.2.0) cannot burn the bootloader to this chip as it attempts to set the high fuse bits, which cannot be done. Unsure why this still isn't fixed. Typical error message:

avrdude: WARNING: invalid value for unused bits in fuse "lock", should be set to 1 according to datasheet
This behaviour is deprecated and will result in an error in future version
You probably want to use 0xff instead of 0x3f (double check with your datasheet first).
avrdude: verification error, first mismatch at byte 0x0000
0xf3 != 0xcb
avrdude: verification error; content mismatch
Failed chip erase: uploading error: exit status 1

Start by reproducing the Arduino IDE 2.2.0 bootloader-burn attempt on an ATmega32u4 and capture the avrdude command and full output. Trace where the IDE configures the fuse values, then verify the fix by successfully burning the bootloader without the reported fuse verification error.

Written by the indexing model from the issue text.