It uses 1.1.1.1 for itself, and hands out the pihole ip for DNS through DHCP.
That said, I think I fixed it. In my previous configuration, I had the router handing out the pihole as the primary DNS, and then (without much thought) I had set the secondary and tertiary DNS servers as 1.1.1.1 and 1.0.0.1.
A few days ago, I realized this was superfluous, and removed them, leaving only the primary. Since then I have had no problems with local hostname resolution, and my mobile ads were more consistently being blocked! It likely affected my Linux machines as well, but I wouldn't have noticed because they have adblockers. It's strange, though - pihole was definitely blocking (I had to frequently whitelist domains for my wife's work) before these changes.
So I think I'm ok now - thanks for your help, everyone! And Graysky, see you in Archland.