So the good news is that today, with updated hardware, bootloaders, firmware, and IDE
these 3 issues should no longer be a problem.
That indeed may be the case. Also many (myself included) now enjoy the ability to operate without a bootloader at all using the upload sketch using programmer option the IDE version 1.0.x now grants. I find myself using it more and more for various reasons. So if one has the means to reburn a bootloader in the first case, then they also have the ability to upload sketches without even needing a bootloader.
Lefty