I just re-read the whole discussion and thought it would be useful (for me, at least) to summarize it.
The original bug report was that NM+dnsmasq and standalone dnsmasq are incompatible because they have overlapping network socket address ranges, 0.0.0.0:53 and 127.0.0.1:53.
One solution is for the administrator to comment out "dns=dnsmasq" in /etc/NetworkManager/NetworkManager.conf.
Another solution is as described by the submitter's title: "[Hey NetworkManager,] Don't start local resolver if a DNS server is installed".
Another solution favored by Mathieu is for the NM-enslaved dnsmasq and the standalone dnsmasq to use disjoint network socket address ranges.
Early on, Mathieu said that solving this problem would not be a top priority because not many users want to combine the DNS server role (running bind or dnsmasq) with the DNS client role (running NM+dnsmasq).
Alkis argued that the incompatibility is a serious bug that should be prevented using package dependencies or eliminated automatically by maintainer scripts or other means. The administrator shouldn't have to search the web to figure out how to make the dnsmasq package work. Troublesome is the fact that standalone dnsmasq sometimes works, sometimes doesn't, in the presence of NM+dnsmasq.
Along the way Alkis levelled some fundamental criticisms against the design of NM+dnsmasq.
I think that there is a clash of civilizations here: the Debian way (modular components that just work together in any combination allowed by package dependencies) versus the RedHat way (big daemons with limited options that own subsystems).