I am still on Fusion 8.5.10 with a Sierra 10.12.6 host. But I have a High Sierra 10.3.6 VM that is running with APFS (see screenshot below).
Not exactly sure what the secret sauce is to get the APFS running inside a High Sierra VM. But I would think one requirement is that the VM is stored on SSD otherwise it won't be seen as virtual SSD by Fusion and the guest VM. (Note in the screenshot, it shows Medium Type as SSD).
This High Sierra VM started as a Sierra VM with fixed allocated virtual disk, split in multiple files and virtual SATA controller. It also has
devices.hotPlug = "FALSE"
ahci.port.hotplug.enabled = "FALSE"
in the vmx configuration file.
It got upgraded to High Sierra through Apple Software Update, if I recall correctly on version 10.3.4, but an earlier version upgrade attempt did fail. I don't recall having to explicitly choose APFS during the upgrade process.