Although my first reaction was, I confess, negative, I can see some benefit in this approach as it works well for those apps that want to use it, and imposes no penalty at all for apps that want to ignore it.
It still, however, leaves open the option of a separate “EEPROM manager” sketch which could be used to enable EEPROM load/save in apps that do nothing to support it. In an online library of apps, possibly as hex files, the only thing needed is a flag on the description that says whether or not an app includes EEPROM use, and then if it has EEPROM self-management.
Here is a tutorial, not for the Leonardo but should be close, on reading EEPROM and dumping to the serial output (which if memory serves on the Arduboy/Leonardo defaults to USB Serial). Comparable code can read from serial and place in EEPROM.
The nice thing about this option is that the serial usb will always be present because that is how the Arduino IDE updates the device. There is no additional penalty for using USB serial in your sketch beyond the (usually small) amount of code you write yourself.
At this point, my one standardization suggestion would be a char item in the reserved area that can be set to identify the current owner of EEPROM. A dump option will just create a 1K dump via serial, which can be captured as a 1K file. External tools (more power, more space) can then take on the job of “EEPROM library management”, using the “EEPROMowner” tag as a base for deciding how to handle things.