Solved!
I got on the phone with a technical representative from Remy Delco. Nice guy. We talked about the Leece alternator (he was familiar). He shared that there is a compatibility chart that states which of their alternators work and don't work as a drop in. Because I had removed the DUVAC requiring components (moving to DC-DC controlled charging), I was a free agent and that the 28si is a solid choice.
Here's the key difference.
The 28si IGN stud IS bi-directional. It can take 1amp in and it pushes 1amp out. As he put it, it is for running indicator lights in most applications.
Solution: Remove the IGN wire and tape the connector at the end of the IGN wire. Boom. Worked perfectly, no alt warning light, and everything ran smoothly.
I'm not sure this is the fix for everyone, but the 6v relay seems to still get that 12v IGN power via the rest of the circuit.
Bjohnsonmn's post in Engine won't stop! (Post DUVAC replacement, 28SI) was marked as the answer