This has negative implications for security. For instance, one reason why DNS resolvers might block or modify requests is to blacklist domains used for malware

This has negative implications for security. For instance, one reason why DNS resolvers might block or modify requests is to blacklist domains used for malware operation (botnet C&C domains). Other things like DNS sinkholing and poisoning are also frequently used as tools to disrupt malware communication. In addition, collection and analysis of below-the-recursive DNS traffic is one of the primary ways in which security researchers discover the infrastructure of botnet networks. Overall DoH is probably a net positive, but I don't see downsides like this being discussed.