Alkis: Why do you need the dnsmasq package at all? You want NM and dnsmasq. Why not just use the NM-enslaved dnsmasq?
If the latter doesn't meet your needs, could it be adapted somehow to meet your needs?
Assuming that there are good reasons for using NM and standalone dnsmasq, I'd be inclined to agree with Alkis (if I understood him correctly) that a good solution would be to put the NM-dnsmasq integration stuff into a package and make this conflict with the standalone dnsmasq package.
Alkis: Why do you need the dnsmasq package at all? You want NM and dnsmasq. Why not just use the NM-enslaved dnsmasq?
If the latter doesn't meet your needs, could it be adapted somehow to meet your needs?
Assuming that there are good reasons for using NM and standalone dnsmasq, I'd be inclined to agree with Alkis (if I understood him correctly) that a good solution would be to put the NM-dnsmasq integration stuff into a package and make this conflict with the standalone dnsmasq package.