Bug#745587: base: Cloud AWS EC2 Image will not reply to packets received on additional network interface (ENI)
Still seeing this on the Debian 8.6 AWS release.
bootstrap-vs does appear to include the configuration that handles this on Amazon Linux:
Which writes the correct ip rules and routes to, e.g., /etc/sysconfig/network-scripts/route-eth1, but this file does not appear to be consumed by Debian (on Amazon Linux it appears to be loaded by /etc/sysconfig/network-scripts/ifup-routes).
I hope this additional information is useful.