Okay so I have found the issue pertaining to dns resolution on Ubuntu
16.04.2! There is a critical bug in the package dnsmasq-base here:
https://bugs.launchpad.net/ubuntu/+source/dnsmasq/+bug/1639776 The fix
hasn't yet been applied to the current version of dnsmasq-base.

This time I have all the dependencies on 1.2.6 at their newest version
and installing the patched .deb version provided by Harald Rudell fixes
DNS name resolution on wakeup/suspend and with restart of the network
manager, all while cooperating with openvpn. I hope this helps anyone on
16.04.2 LTS!

wget
https://bugs.launchpad.net/ubuntu/+source/dnsmasq/+bug/1639776/+attachment/4780245/+files
/dnsmasq-base_2.76-4ubuntu1FIX1639776ubuntu1_amd64.deb

sudo dpkg -i dnsmasq-base_2.76-4ubuntu1FIX1639776ubuntu1_amd64.deb

This appears to have actually worked, and is much better than using
dnscrypt-proxy (which I have found to be incredibly slow) or holding
back a bunch of packages.

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https://bugs.launchpad.net/bugs/1636395

Title:
  dnsmasq not working with OpenVPN

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