I'm completely unfamiliar with unikernels, but I just skimmed a brief description. My first question is: Do they still incur the overhead of running against a Hypervisor like common virtual machines?
Also, possibly a clairification: Unless I'm misunderstanding what you mean by "running several linuxes on a linux machine", I believe you may be mistaken about the way containers work. Only one Linux is really running. And that is the Linux that the kernel comes from. The other stuff doesn't run unless you tell it to (so, no init, no daemons you don't specify, etcetera). Yeah the image size can be a little fat if you don't trim them down, but you can have a container nearly as small as your code is, if you statically compile. On the order of just a few bytes of overhead.
Also, possibly a clairification: Unless I'm misunderstanding what you mean by "running several linuxes on a linux machine", I believe you may be mistaken about the way containers work. Only one Linux is really running. And that is the Linux that the kernel comes from. The other stuff doesn't run unless you tell it to (so, no init, no daemons you don't specify, etcetera). Yeah the image size can be a little fat if you don't trim them down, but you can have a container nearly as small as your code is, if you statically compile. On the order of just a few bytes of overhead.