What about Xen? I guess it's going to depend on whether you consider a baremetal hypervisor an OS and virtual machines a form of container, but it does have a microkernel design and is popular in its niche.

Is the lack of support for containers in, I'm guessing QNX, because of the design making this difficult/impossible or just the result of a lack of popularity?

Except this is because containers, as they arw commonly referred to, are an image of software compiled for linux + linux kernel specific technologies for running them (cgroups, namespaces) etc.

Nothing stops a microkernel from having gitten popular and then having got it's own implemented containers. Linux won because it was first, not because monolithic is better.

What is the most popular unix like microkernel?

Macos is monolithic. Technically it's "hybrid" but from a security architecture perspective hybrid suffers from all the same flaws of monolithic.

Linux containers are a security nightmare. The linux kernel has so much attack surface they add that constantly causes privesc cves, and it's especially annoyimg when they break out of the container to the host. Literally 3 of the recent 0days wouldn t work if you disabled user namespaces, which are needed for rootless containers.

So nowadays, every cloud provider runs "containers" that are actually vm's, in order to receive the same security that a microkernel would provide.