Also, what do you mean my "standardizing dnsmasq behaviour?" From my recollection of using it (and from manpage[0]), it's pretty basic. You (1) manually edit /etc/resolve.conf to point to localhost dnsmasq instance (2) use app-specific ways to configure nameservers, in dnsmasq's case it's an ad-hoc list of secondary resolv.conf files specified on command line, with no defaults. I don't think this is worth standardizing, as this scheme cannot even represent network interface -> dns entry associations.
Well, many people are confused about how DNS resolving works. Many of do not consider a problem, when they configure their resolv.conf to two different upstreams, each returning different answers (i.e. one responding for domains that the other doesn't) and then wondering, why stuff is broken.