Hypervisor.framework provides only the bare necessities: the ability to manage vCPUs, stage 2 page tables, and handle hypervisor exits. It does not do any sort of virtualization except for the CPU itself (which, on ARMv8, is very little due to hardware providing good primitives already). Virtualization.framework is full operating system virtualization suitable for running modern Linux and macOS guests.
AFAIK Virtualization.framework is built on top of Hypervisor.framework. Former is high-level one allowing you to create Linux VM with few hundreds lines of code. Latter allows you to run your whatever you want with few tens of thousands lines of code, but absolute freedom when it comes to drivers and every low level detail.