Given some directory layout under the current working directory like pkg/a/a.proto and lib/b/b.proto, this protobuf protoc invocation succeeds: protoc --go_out=tmp -I pkg -I lib a/a.proto. Note that the argument "a/a.proto" is not a path to a file in current working directory and is relying on being resolved using -I pkg.

The corresponding buf protoc invocation looks like it is not using the -I pkg to resolve its arguments:
buf protoc --go_out=tmp -I pkg -I lib a/a.proto returns

path "/Users/david/code/protodemo/a/a.proto" is not contained within any of roots "/Users/david/code/protodemo/lib", and "/Users/david/code/protodemo/pkg" - note that specified paths cannot be roots, but must be contained within roots