The only reason for the System to address the SE/30's Video Subsytem at all is the Video ROM/DeclROM being detected by the Slot Manager at startup. Folks have made your same point about the SE/30 somehow loading registers in the onboard video subsystem causing a problem, but very doubtful that can be the case.
Cannot imagine how such could happen as the Slot Manager only addresses slots detected via DeclROM. PseudoSlot at $E only becomes problematic with onboard video's introduction in the IIci/IIsi generation in the Mac II series.
Back to the DuoDock as a $E expansion card. Onboard Video/LCD display at $E is disabled in the DuoDocked/MiniDocked, replaced by Video Substems in those docks.
The way I'm seeing it, pulling Video ROM will equate with a Docked State, leaving $E available for use via DeclROM on a NuBus Card. The SE/30 has no idea that there is anything to load at that Slot Address.