I managed to mute the beep, so it's possible. As for pressing Ctrl-D on each reboot it's less of a burden, IMHO, than pressing keys to get to a BIOS menu, which is something I often do on older computers when booting from USB. Unless things have changed, /usr/local does not get wiped. If using an opinionated chroot written by someone else, e.g., Crouton, maybe the risk goes up, not sure. But setting up own chroot in /usr/local will protect anything intended to be permanent. If only pressing Ctrl-D on reboot, it's not easy to wipe anything accidentally. Replacing the bootloader with an open source one that's easier to control is the best solution, e.g., coreboot from https://github.com/MrChromebox