You have an extra file in /etc/dnsmasq.d directory. The file is 02-custom-settings.conf.save.
This .save extension is usually added by text editors, like nano, pico and others.
These .save files contains temporary saved text (a backup of the original file) when you are editing a file.
Your log shows you actually have 3 versions of the same file (the original and 2 backups), causing the repeated keywords: