Just tried the old and the new for a DCA-DEN trip. I was trying to maximize miles, so wanted more, not less stops.
The old matrix gave me a DEN-PDX-ORD-DCA flight. The new matrix didn't.
If it's the same engine, what happened? I entered "UA+" in each case, got multiple cities in each case, but missing the flight with the highest mileage in the new version, which is what I was looking for.