Adding both the PCI-E graphic card and the USB device while the VM was powered off worked well. Both of them could function normally. So that may seem to rule out 1, 2 and 3. As of 4, hot-pluging USB failed even when CPU, RAM and storage, of both the VM and the host, were quite enough. As of 5, as PCI-E passthrough were configured while the VM was powered off, no hot-pluging PCI-E device were involved.
I see there are restrictions while PCI-E passthrough is enabled, including suspending, migrating with vMotion, or taking or restoring snapshots. But hot-pluging USB device via arbitrator is not mentioned in any documentation as an restriction with PCI-E passthrough present.