westfw:
I am getting a little worried at the number of copies of Optiboot for 1284 that are out there. (All with the same version number? But not necessarily the same code?) It's bad enough that the Optiboot repository and the Arduino repository are modified independently (and it's pretty tough to get patches from Optiboot into Arduino, just due to momentum and manufacturing issues.) But now there are three or four copies of the 1284 optiboot out there... (Maniacbug, jbaum, crossroads, goldilocks)
I can see your concern. However, no modification is being done to optiboot itself, only extra bootloaders and custom pin configs being added. In my case you will be able to download optiboot and download my fork and they will be identical with the exception of the extra options I add. You will still see all the [optiboot] devices which will contain all the same settings and bootloaders as the original. This is tracked on google code so you will easily be able to see which files are modified.
Since arduino has not fully integrated Optiboot, included 1284, and allowed for quick easy pin configurations I really see no other way.
Unless you have the know how and download optiboot and compile your own. Which I did mention earlier I thought that a good tutorial on how to do so may not be a bad idea.