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Afaik, some apps like Netflix that rely on geo-blocking for their content licensing do it already and it's only a matter of time until they switch to DNS over HTTP so requests cannot be altered at all.

That's just going to break functionality on many networks.

I set up a rule on my router to drop any DNS traffic and DoH traffic to well known DNS providers unless it comes from the server running pihole. Otherwise it was proving very hard to find out how to force applications / mobile devices to use my DNS server.

you could also just NAT port 52 to your pihole. (translating 8.8.8.8 ofcourse).

I don't know if this would work with DoH. (but DoH is terrible anyways)

That only works as long as you can easily distinguish the DNS traffic from the rest, right?

For instance if my VideoApp serves content from videoapp.example.com and I use my own DNS also at videoapp.example.com, served over DoH, I think that's basically the end for host-based content blockers.

There are block lists for DoH servers and other DNS queries can be forwarded to your own resolver.