The EESAV fuse only effects the function of the Chip Erase command. It is impossible for this feature to be used when uploading with the bootloader, because that would erase the bootloader as well as the old program.
This is correct behavior - uploading an new sketch doesn't trash anything you might have in the eeprom. The bootloader used does not support clearing the eeprom - it won't fit in 512 bytes of you add that functionality - so -e or no -e, uploading via opinion won't clear the eeprom. I'm not at my desk so I can't confirm, but looking at platform.txt i don't think -e is used for normal uploads. Chip erase is an ICSP command anyway - it clears the entire flash including the bootloader (note that it can only be executed via ICSP or hvsp, not through bootloader)