I gave this bug a test run, performing a debootstrap both ways (as root and in a fakeroot) and, on my test machine (Debian 9) with insserv 1.14.0, both methods work. That is to say, both chroot environments end up with the init symbolic links in their etc/rc?.d/ directories.
This suggests to me that either the bug has been fixed (possibly in debootstrap since we didn't address it in insserv). Daniel, could you please try this again and let me know if the issue persists? If it's working for you now we can close this report. - Jesse
