The biggest and most consistent downside I see with these DNS enhancements is that it prevents filtering at the network level. Querying nameservers is being pushed into applications themselves to support these new features (such as Chrome and Firefox), which bypasses any system resolvers configured on the host. In most cases there is no way to signal from the network that it is not desirable to do this (Firefox being…
When enterprises own the devices on their networks they can add whatever root certificate they like and MITM filter whatever they like. This makes over the network traffic more secure and does nothing to really impact threat detection. If you don’t own the device then 1) should you be interfering or snooping the traffic at all? 2) if you need to limit threat then subnet clients you don’t own.
For your basic premise to work, it also means that the MITM middleboxes will need to support the DoH protocols and support recording, and filtering those responses.
Additionally, custom roots certificates will only work on devices that you can actually set a custom root certificate for, a great example is IoT devices. Is your TV suddenly talking to a botnet or was that a legitimate update?
We can argue about whether those middleboxes are even sane to deploy (hint: they're not), but what is historically true is that they are known to update slowly to new protocols, if at all and are known to cause compatibility issues for traffic that is inherently expected to be unchanged. They're enough of a problem at the _TCP_ layer that QUIC was explicitly designed that minimal information is available in the protocol headers so middleboxes would have less to mess with.