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If you don't want your system to use those entries in your host file, why can't you simply remove them? Do you have other enteries in your host file that you do need to be served? You could just have DNSMasq skip the system-wide host file --no-hosts, and you can point DNSMasq at an alternate hosts file that has the entries you want --addn-hosts. -h, ...
I dont know whether dnsmasq supports this or not, but from the description of what you are trying to achieve, it sounds like setting up bind would be a more elegant solution. That way, you can keep your hosts file and DNS forwarding / resolution completely separate.
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