Quick thought. If software wanted to, could they not, today, bypass your DNS resolvers anyways? Choosing to use DoH on software where you control the DNS resolution seems like an unambiguous win. FWIW, the Chromium implementation of DoH upgrading only upgrades you to DoH if your configured DNS provider is known to support it via a hardcoded list.
In theory, you could have Pihole resolve using a DoH resolver and your devices resolve using Pihole and have the best of everything.
(Disclaimer: Google employee, not working on ads or Chromium or DNS.)