Unfortunately, the ATmega32U4 and family are the AVR chips that have received the least amount of coverage by 3rd party platforms, and never got the blessing of the MCUdude/DrAzzy treatment. The only one for this family I'm familiar with is HoodLoader, which is more focused on a specific use case for these chips.
However, the EEPROM erasing behavior you want is default in even the official Arduino AVR Boards platform. You can see here that the EESAVE bit is unprogrammed in the configuration fuse setting for the Leonardo, and the same for the other ATmega32U4 boards of that platform:
So the only thing you miss is having a menu to control the behavior. If you are wanting that, it can easily be added on to whatever platform you are using already, using the custom board options system like how it was done in the MCUdude and DrAzzy platforms: