Only the dnsmasq binary is installed as a NM dependency:
$ dpkg -S bin/dnsmasq
dnsmasq-base: /usr/sbin/dnsmasq
$ apt depends network-manager
[..]
Recommends: dnsmasq-base
The systemd service unit for dnsmasq is contained in another package that isn't installed:
$ dpkg -S dnsmasq.service
dpkg-query: no path found matching pattern *dnsmasq.service*
$ apt-file search dnsmasq.service
dnsmasq: /lib/systemd/system/dnsmasq.service
$ apt policy dnsmasq dnsmasq-base
dnsmasq:
Installed: (none)
[..]
dnsmasq-base:
Installed: 2.89-1
[..]
I had a go at it below replacing the dnsmasq binary with the pihole-FTL binary (via symlinking) but the later seems to be missing a Dbus dependency to go forward:
As port=0 was tried already in above thread, you could try configuring another unused port.
Grep for it:
sudo rgrep -i dnsmasq /etc/NetworkManager/
See also:
man NetworkManager.conf