bhyve: Treat the COMMAND register for PCI passthru devices as emulated

Don't pass through writes of the command register through to the
physical device. These registers do not need to be in sync, and in
some cases (e.g. when the guest is sizing the BAR and temporarily
disables decoding), the states need to diverge.

PR: 205549
Reviewed by: corvink
Sponsored by: Chelsio Communications
Differential Revision: https://reviews.freebsd.org/D46179