The main limitation of Cap'n Proto compared to Protobuf is the ecosystem -- missing or poor-quality implementations in many languages, limited tooling, etc. Admittedly this is probably a showstopper for most users. It's also the hardest thing for any new contender to solve.
With all that said I would tend to agree that benchmarks are probably pointless. I've spent a lot of time benchmarking serialization and one thing I know is that benchmark results will vary wildly depending on the use case. A benchmark of an example/toy use case isn't really indicative of performance in a real use case.
(I'm the author of Cap'n Proto. I don't know much about Flatbuffers so can't comment there.)
When I created Bebop years ago I tried to benchmark it against Cap’n Proto, but the lack of a semi-decent web or C# implementation mentally made me recategorize.
So I suppose I’m just comparing what’s closest in terms of ecosystem support rather than a purely functional level.
It obviously doesn't make sense to benchmark a JavaScript Bebop implementation against a C++ Cap'n Proto implementation, nor does it make sense to compare against a JS Cap'n Proto implementation written by a third-party contributor that is incomplete and unmaintained... so there isn't really a sensible comparison to make.
Flatbuffers immediately compares itself to protobufs as well on the front page.
They aren’t relevant to what Bebop is doing and thus no benchmark or comparison can be made between them.