Well, I think it makes sense given the history. When seccomp-bpf and the other stuff was introduced, there was already a BPF VM in the kernel designed to efficiently run untrusted code (although seccomp-bpf can't use the JIT today); adding another VM is a maintainability and security hazard, and simplicity is good for security, so why not adapt it?

And now that it exists, it makes sense to evolve the bpf design to be more efficient but keep the result backwards compatible and unified between subsystems.