Lycoming publishes Service Instruction 1569A setting out a roadmap for dual E-mag installation in certified aircraft:
“Replacing both magnetos with two EIS units is considered a major alteration that is a major change to
the type design at the airframe level and would require an airframe type certificate, amended type certificate,
or supplemental type certificate approval. When running dual EIS, the second EIS must be connected to a
backup power source independent from the aircraft’s electrical system. A backup battery system such as the
TCW Technologies™ Integrated Back-up Battery System has been evaluated by Lycoming and found to be
acceptable for this requirement.”
Don’t they, at the same time, suggest, if not outright say, that dual electronic ignition would be a major alteration to the TCDS, thus require an STC?
They say exactly that in the quote I posted that comes straight from the SI.
OK, so it needs an STC.
But just because something is a Major doesn’t necessarily mean it needs an STC. For example you could do a Field Approval. Probably moot in reality since nobody would install the product unless Lyco produce the STC, anyway 
A Major Alteration can be done by Field Approval. A Major Change to Type Design is not the same as a Major Alteration and will require either an STC or change to the TC.
Well, yes, but in reality anybody installing this is going to run away at 150kt unless there is an STC… after all, don’t we know that some percentage of mechanics won’t install a Concorde battery in place of a Gill one without an STC 
Lycoming state verbatim in SI 1569A (local copy)
Replacing both magnetos with two EIS units is considered a major alteration that is a major change to the type design at the airframe level and would require an airframe type certificate, amended type certificate, or supplemental type certificate approval
