Hello,
extra-aarch64-build -c results in a chroot that does not have the package databases for the alarm and aur repos downloaded, the former of which is required for extra-aarch64-build to actually work on some packages, namely linux-aarch64.
I'm not sure which part of the conga line of shell scripts is in charge of refreshing the repositories, but this should be an easy fix once the right point is found at which to do the -Sy(u)
EDIT: Upon further investigation, it looks like the problem is that something along the line copies in a pacman.conf that has those repos missing. /usr/share/devtools/pacman-extra.conf needs to be patched, I believe.