I would think that the Patriarch (and the Pope) would regard Coptic Christianity as heresy, given their rejection of the Council of Chalcedon. While they may not have (or continue) to see themselves as Monophysites, that's how the orthodox churches saw them (incorrectly, I guess). I think it's better as it is now, so I'm not complaining, but the previous setup was accurate to an extent, at least from the Catholic and Orthodox position. But they would probably regard Miaphysites as heretics in the same way they regard Arians as heretics; rejection of an Ecumenical Council was no small thing.
All the Christian religions is heresy of Orthodoxy!!1!
Honestly, though, the distinction between "X as heresy of religion Y" and "X as separate religion in the same group" seems rather bizarre if it's meant to be indicative of something inherent to the religion. I know very little about the heresy mechanics in this game, but if it's anything like EU3, heresies are just religions the devs spent less time on. When they release a patch/DLC giving that particular creed more love, it gets promoted to a "full" religion.