if that is also true for the 1284P fuse settings.
I don't think we can blame the Arduino team for the 1284P fuse settings...
I dunno. You have to change the fuses to upload programs without the bootloader anyway; if you know enough to do that, you should make sure they're all the way you want them to be.
I wasn't implying it was the Arduino team, just if the settings have been derived then it would explain some things.
I initially set the fuses by burning a bootloader to new uC's. In some cases I then wiped the bootloader by programming directly via ISP.
Checking the 1284P maniacbug fuses does show that EESAVE is unset.
Revised fuses (incorporating Full Swing Oscillator and Preserve EEPROM through chip erase) for the 1284P would be:-
LOW FUSE : 0xf7
HIGH FUSE : 0xd6
EXTENDED FUSE : 0xfd