Export Compiled Binary - Difference between hex files with and witout bootloader

That's my understanding also, though I've never tried it. I did a quick skim of the other thread but I don't understand why it wasn't working. Yes, you need the fuses set for the bootloader, but the fuses on an Arduino should already be set correctly. Even when you do Upload Using Programmer it still leaves the fuses the same as they were set when you do a Burn Bootloader.