Currently a HVM with PCI passthrough and Qemu Linux stubdomain doesn’t support MSI-X. For the device to (partially) work, Qemu needs a patch masking MSI-X from the PCI config space. Some drivers are not happy about that, which is understandable (device natively supports MSI-X, so fallback path are rarely tested).
This is mostly (?) about qemu accessing /dev/mem directly (here: https://github.com/qemu/qemu/blob/master/hw/xen/xen_pt_msi.c#L579) - lets discuss alternative interface that stubdomain could use.