Well, I do have the external programmer, so that would solve it for me.
But for any level of distribution to Arduboy owners, it's a non-starter.
I'm curious about the startup sequence, because the Arduino loaders long ago stepped over this problem and, as far as I can tell, jump straight to the sketch with no delay, and only delay for a software load on a reset button. I had to carefully do a "wire reset" on a "beetle(leonardo) compatible" (thing is the size of my fingernail!!) to load new software.
So, let me theorize for a moment here about what would resolve this and help a few other issues at the same time.
1) Bootloader start screen shows a logo and does a sound chime, acting as both basic test (screen, sound, led) and ensuring positive bootup.
2) Bootloader start screen has a time-limited prompt to bump to "load mode". Once in load, mode, the Arduboy stays there until rebooted. Easy to upload new sketch at that point.
3) Sketch upload is driven by well documented (easy for Win/Linux/Mac) transfer of a .hex or equivalent file, meaning binary distribution is possible and a portable loader (possibly from host mode OTG phone) can be implemented.
4) This bypasses offer of any USB capability unless user requests it, eliminating spurious driver load requests on host system.
5) Try and keep bootloader under 1K, or at least under 2K.
6) New bootloader can be loaded via a sketch, so as to not require special wiring or hardware, allowing deployed units to be easily upgraded.
That #6 is a concern. I am assuming that it is at least possible - but tricky - to update the bootloader without a programmer, but I am beginning to think that all of the techniques I see don't actually skip using a programmer, they just skip using a dedicated programmer and find a different way to drive the ICSP connection. I was rather hoping that a dedicated sketch could be loaded that would contain the new bootloader, and then on command, cross write the bootloader from sketch area to actual bootloader area. But - still out of my depth to deal with that question.