It's running pretty good. However, some things I changed in the meantime:
The fans in the JBOD expansion boxes run nearly at full speed all the time (this powerboard has no temperature sensor) and cry like hell. But the JBODs don't need so much cooling. So I removed the two fans in the back. In addition I replaced the three fans in the fan wall with Supermicro FAN-0074L4 fans (green ones, direct replacement possible). However, I would not do that in a warm environment.
The "copy large files from bare metal to VM via SMB problem" is still there. I changed copy direction and do fetch files on bare metal from VM now, always, always, always.
I do not mount all these drives in Unassigned Devices. I created individual User Scripts for all mount and unmount commands. This way they don't show up on the Main page. I experienced a lot of problems if the Main page refeshed before all mount points were collected and shown.
Starting the whole stuff is a manual activity:
1. Physically start the JBODs.
2. Physically start the bare metal server.
3. Do not start VMs automatically on bare metal server (starting two Unraid VMs at once did result in some problems with USB license sticks).
4. Automatically start only those Dockers (bare metal and JBODs) that don't need access to the other servers.
5. On bare metal server manually start the VMs one after another and wait til completion (JBOD web GUIs are reachable and their arrays are started).
6. Mounts in VMs to bare metal server automatically start with JBOD arrays (mount/unmout commands in User Scripts attached to Array Start/Array Stop).
7. Mounts in bare metal server to JBODs are started manually after the VMs are up and running.
8. Now start all those Dockers on bare metal server manually that need access to JBOD mounts.