After they have a couple generations of laptop silicon under their belts, there's nothing stopping them from dogfooding a real server macOS for awhile and booting up an Apple Service Cloud.
No special insight into whether they actually will, but it's a natural play.
There’s also an issue of margins. Apple sells attractive hardware and provides a software ecosystem, and they charge high margins for it. Big server users use a large numbers of servers, and they want a lot of bang for their buck. This is not a game that Apple has historically played very well, nor do I see why they would want to.
Darwin, macOS Server. This sounds fun.
Yet Apple has quite the powerful chip family. If they were to spin off a subsidiary without the consumer-focused mission...well, that's what I would do!
Apple isn’t really in the server business, and the kinds of high performance VMs that want direct hardware access seem unlikely to run on Apple silicon in the near future. It seems to me that virtualization could work just fine without an IOMMU in this scenario. (Certain GPU workloads would be an exception.)
That being said, I would expect Apple to have an IOMMU at launch for a different reason: Thunderbolt or any other external PCIe connection. Doing this without an IOMMU is a security catastrophe, in contrast to doing it with an IOMMU, which is merely an enormous attack surface that no one secured properly.