Why not just use the Veeam Agent for Windows in Free mode? Yeah, it'll be separate jobs for these VMs, but honestly, it's just a limitation of VMware; you can't snapshot machines with passthrough devices. Go try it quick just in vCenter if you haven't yet.
Like if someone led you to believe that these could be backed up, that would be another story, but it's pretty clear from the get go both on Veeam's pre-reqs. and the VMware pub guide on PCI passthrough that you can't snapshot them.