Your router can proxy encrypted DNS (if you have some decent firmware) or you can set up your own DNS server. There are also things like nextdns.io which can do all the work that a pihole does but works outside your home network.
I think the point is that some applications will use DoH/DoT/a custom protocol to bypass DNS-based blocklists. It's trivial to run your own DoH/DoT/custom server if you just hardcode the IP into your application.
You can still block those by doing IP-level blocks for known ad domains, but that starts to become a problem if one of those domains are run from a shared cloud host (i.e. Cloudflare etc.) because you will also block legitimate domains.
Most in-app ads and tracking will still use HTTPS so if you use SNI sniffing + certificate validation (to prevent domain fronting) you can still do network level blocks, but that's quite resource intensive, especially at modern internet speeds.
