@Josh: There is no script; NM executes dnsmasq directly.
But this might help you:
network-manager (0.9.6.0~git201207271115.edb85e9-0ubuntu1) quantal;
urgency=low
* upstream snapshot 2012-07-27 11:15:54 (GMT)
+ edb85e972051aff3cfcd5990ea1bd8a28dddc9d9
- dnsmasq: allow custom configuration via /etc/NetworkManager/dnsmasq.d
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https://bugs.launchpad.net/bugs/1010724
Title:
NM fails to start dnsmasq such that it listens on ::1
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