If that is the case, you should not be relying on an opensource platform to be developing your project.  It is constantly evolving and not guaranteed to provide you with anything.

That being said, the bootloader is completely independent of the Arduino IDE.  It would be useless to bypass the bootloader because the IDE is not classified as a final release.

It would be nce if we were privy to the plan?

Join the developers mailing list... you will know what is happening.  Instructions for joining are somewhere in the wiki.

What if someone was given the pre-compiled hex file by someone else?  In this case they would not have created it in another IDE and would still need a way to get it to their Arduino without the complications of Avrdude.