Network Manager does: --conf-file=/dev/null 
--conf-dir=/etc/NetworkManager/dnsmasq.d
and might therefore be an example of those that call it - as you mentioned it 
can be discussed if it would have to add the,*.conf or anything like it.

An example of a program not calling with --conf-dir=/etc/dnsmasq.d might be 
libvirt.
But then it explicitly wants no other config at all to influence it and in 
terms of the interface exceptions and such it is correct as it explicitly 
states the interface to bind to.
Call:
--conf-file=/var/lib/libvirt/dnsmasq/default.conf
But in there:
interface=virbr0
So instead of using exclusions it it very specific where to bind to.
Maybe that and similar cases are a reason why it should not always pull in the 
dnsmasq.d dir - not sure?

Could you list the other examples you found - as I assume to get an idea
of potential side effects we would have to collect as much as possible.

** Changed in: dnsmasq (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/1652032

Title:
  ambiguous config file

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