I did the same search but with forks excluded to reduce noise. Manually excluding the false positives where the rule isn't loaded from rules_proto and trying to group by org, I see the following repos:

https://github.com/envoyproxy/envoy
https://github.com/envoyproxy/envoy-openssl
https://github.com/google/cel-java
https://github.com/google/skia-buildbot
https://github.com/grpc-ecosystem/proto_processing_lib
https://github.com/privacysandbox/bidding-auction-servers
https://github.com/privacysandbox/protected-auction-key-value-service
https://github.com/privacysandbox/data-plane-shared-libraries
https://github.com/abitofhelp/apis-rust
https://github.com/abitofhelp/bazel7_go_grpc
https://github.com/abitofhelp/bazel_grpc_pbuf_go
https://github.com/world-federation-of-advertisers/cross-media-measurement
https://github.com/world-federation-of-advertisers/local-market-configuration
https://github.com/world-federation-of-advertisers/common-jvm
https://github.com/stackb/rules_proto
https://github.com/EngFlow/engflowapis
https://github.com/rendezqueue/rules_sxproto
https://github.com/bulwark-security/bulwark

proto_descriptor_set Bazel rule missing #19647

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