I'm a noob, but.. there definitely seems to be something wrong.

I had DoH working with 1.1.1.1.
Then I decided to dabble with a PiHole.
I set my DNS to the PiHole and press Apply... great, everything works!

...a dayish later?...

I'm back to resolving via Verizon. TL;DR if I goto the webfig page for DNS and simply press Apply -- leaving the existing server IP as-is -- then boom, all my clients are using my pihole again.

For about a dayish.

That sounds like the expiration of a DHCP lease to me. Updating the DNS addresses in DHCP doesn't apply them instantly throughout your network; each client keeps using the old information from their current lease until it expires.

Moreover, if the client reappears and asks for the same lease before it expires, I believe the RouterOS implementation simply tells the client to keep using what it already knows. Updating the DHCP configuration doesn't rewrite all the stored leases on the DHCP server! You have to wipe out all the dynamic lease info when you reconfigure DHCP to force all of that to be regenerated: