After some quick testing, I believe I found the problem. I had changed the "Upon host shutdown" setting to Hibernate and my Home Assistant VM does not respond to a Hibernate command . Based on the help tip for the "VM shutdown time-out" setting Unraid should attempt to shutdown the VM but is not, preventing the array from stopping. Changed that setting back to shutdown and the array now stops in just over a minute as expected.
Hog_Of-War's post in Unable to clean shutdown was marked as the answer