Probably best to use port-xen now that we think it's a xen thing. I would suggest investigating everything suggested to you and then sending a new message based on your future understanding to port-xen.
1) I am unclear on if the xbd abstraction has the concept of 4K sizes, and if so how that is communicated, and if not how the dom0 is supposed to map things. With any luck, this is supported and the xbd driver in NetBSD is just not noticing the sector size variable and it's a fairly small matter of programming. Looking quickly at sys/arch/xen/xbd_xenbus.c, I see some concept of sector size, but it would take me a while to understand and trace all this. I suggest trying a current or netbsd-10 PV or PVH domU and seeing what happens. 2) In your HVM success, do the disks appaer as 4K within the domU?