Having read this code, I would say any such fears are utterly unfounded. Did you read the code? I have, and there doesn't seem to be anything like this.
No, and that's why I said "if" and "crystal ball". I wouldn't claim to have to the knowledge to fully understand what is in the bootloader.
I've never once suggested that Arduino are up to anything malicious. I don't think Arduino are out to screw anyone or 'close source'. I simply mentioned a potential issue that could maybe arise one day - but quite probably won't by the sounds of it. "Unfounded" is more than fine by me.
And I thank you again for your efforts in looking into that code - you've helped everyone understand a bit better what is going on. Especially me.