If you do want to put the Arduino bootloader on it, you should probably do a lot of testing to make sure it doesn't cause any problems.
Sorry I missed your post.
If they are using it with a Arduino then it wouldnt matter at all because they would have to wait anyway.
Ladyada has a hack which starts the program if anything other than 00 is sent to the bootloader so that would also work.
I might put a SMD jumper on to enable/disable it. Just solder over it to enable.
The K107 looks good but it has a awful number of limitations.
I can steal some ideas from its software though. 