If you require something that couldn’t be used over CloudFlare, that cedes a whole lot of power to what they choose to support

Power is excessively unreasonably ceded when Cloudflare is in the loop. To avoid CF is to put power back where it belongs. Cloudflare-incompatible tech ensures CF does not wield inappropriate power.

any networking could, in theory, be run by proxy.

Indeed, and this frustrates sigsec. Connecting to someone requires trusting them not to do something stupid like hand their keys to a giant centralised corporate overlord. At least avoiding Cloudflare is low-hanging fruit. It’s usually easy to detect when CF is in the loop, apart from a few rare shenanigans where CF uses some IPs that are not in CF’s ASN records.