Pihole v6 defaults to running an ntp server. It is not as feature-rich as ntpd or chrony. Many devices only use sntp, so don't gain any particular benefit from the features available from these.
As you encountered, if something else is already serving ntp pihole detects this and steps back, so leaving ntpd in place is not harmful.
If you want to leave ntpd in place but stop the warning messages then you can disable the pihole NTP server via the webui.
Go to settings, enable expert mode, all settings, timeserver tab.
From there you can disable ntp.ipv4.active and ntp.ipv6.active.