The FlatBuffers encoding is based on vtables and is relatively straightforward (the runtime library is tiny). This also means it's inefficient for small messages, but in my testing its vtable deduplication worked great for my use case (~100k messages of the same type per memory-mapped file), in that the vtable overhead tends quickly to zero.
Cap'n Proto has a more complex encoding that is probably more efficient in terms of wire size, and particularly for small/standalone messages, but the runtime is larger as a result.
Cap'n Proto is both. I.e. you have the serialisation, which can be used on its own, but you can also define interfaces with methods that can pass those serialised structs as parameters, and which return asynchronous promises.