I usually run Gitian directly on whatever host OS I use, so I don't have experience with running it in a chroot.
When I was trying to reproduce the issues using a Stretch chroot and trying to create a Precise VM in it, I actually couldn't get far enough to reach the issues you were experiencing. What command are you using to enter the Stretch chroot (like chroot or systemd-nspawn)?
I would bring the patches up to upstream[0] and see what they think about them.
[0] - https://launchpad.net/vmbuilder
Cheers, Joseph