You can add a custom dnsmasq config line, e.g. to set a local TTL of 60 seconds:
sudo pihole-FTL --config misc.dnsmasq_lines '[ "local-ttl=60" ]'
In case you'd run Pi-hole as a Docker container, you may set its FTLCONF_misc_dnsmasq_lines environment variable.
That option is also accessible via All settings » Miscellaneous as misc.dnsmasq_lines.
If instead you want to keep a bunch of configuration lines in your own custom file under /etc/dnsmasq.d/, you could alternatively enable misc.etc_dnsmasq_d.
All settings is available in Expert mode only.