When programming the atmega32u4(m32u4) EFuse, AVRDude trys to write the upper 4 high bits as "0". These 4 bits are unused by the uP and are to be unprogrammed, set to "1". This causes a mismatch when read for verification since the uP ends up allowing 2 of these bits to be programmed:IE "1 1 0 0 i i i i".
In the avrdude.conf file under m32u4, it is set to write "x x x x i i i i". By updating the avrdude.conf file to "1 1 1 1 i i i i", the upper 4 bits are properly left as a "1" while the lower 4 bits are written according to user input. This corrects the issue.

Example: writing "F3" to the EFuse returns "C3" after programming since AVRDude trys to write "03" and the uP mistakenly accepts 2 of the upper "0"s. After updating the avrdude.conf to default the upper 4 bits to unprogrammed ("1"), the upper 4 bits are properly left as unprogrammed (unused) and the EFuse properly returns as "F3".