Upgrading FreeNAS is designed to work properly. That's "by design". However, there's zero support for RDM and PCIe passthrough "by design" with FreeNAS. Experience shows that RDM is wholly dangerous and it's playing with fire. PCIe passthrough is not "designed" for FreeNAS, which is why there's warnings everything that virtualizing FreeNAS is at your own risk and your own peril. If you make a thread complaining about a problem related to VMs, we'll all point our finger and laugh at you because you didn't listen to the warnings. We aren't overly interested in troubleshooting the problems related to virtualizing FreeNAS. So it is what it is.
*Plenty* of hardware doesn't support PCIe passthrough either. It requires your motherboard to fully support it along with your controller. It also requires the driver for FreeBSD to support the PCIe passthrough properly. And many that claim to support PCIe passthrough exclude FreeBSD. Of all of the controllers I had in my house a year ago, none worked(despite some claiming PCIe passthrough). So if you don't own an M1015, there's a very good chance you'll be forced to buy one(or something else that does work).
Good luck!