i have the same behaviour with my nexus 5x running android 7.1.1.
android completely ignores my pihole - although i have specified it as dns1 and dns2 (leaving dns2 empty always displays, greyed out, google's dns)
my home network supports ipv4 and ipv6.
yet i can see no options to change any ipv6 settings of the wlan in android settings. am i missing something here?