Hello Simon, i am also seeing this exactly error. I was able to nail it down to the very recently update of package dns-root-data in sid. When newer Version of dns-root-data is installed dnsmasq will not start any more with the error messages given.
% policy dns-root-data dns-root-data: Installed: 2015052300+h+1 Candidate: 2017020200 Version table: 2017020200 500 500 http://ftp2.de.debian.org/debian unstable/main amd64 Packages *** 2015052300+h+1 500 500 http://ftp2.de.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status kind regards, Thilo