See, I agree with you on all of these not being suitable heresies, however I don't believe Mandaeism is a suitable heresy either, given that it's a distinct religion in its own right and, as you say, would be akin to making Judaism a Christian heresy, or even the current situation where Manichaeism is a Zoroastrian heresy, which is what started this thread in the first place. I think it would be best to just leave Manichaeism without any heresies like the Eastern religions, if anything simply due to the lack of any movement within the game's time period/location that could be a suitable Manichean heresy.
What about Sabians or Elkasites/Ebonites? In some mods, they were made Manichaean heresies. In addition, some people have proposed making Gnostic groups and movement such as Bardaisanite, Priscillian, Sethian, Valentinian, Simonian and Archontics heresies of Manichaean religion, though these might be pretty farfetched considering that they were pretty much extinct by the time of Early Middle Ages. Someone even proposed that if the devs really want to stretch it, the White Lotus Society in China could be added as a Manichaean heresy, since they mixed Manicheanism with Buddhism and traditional Chinese religious beliefs.
Speaking of the Manichaean sects like Denawars, perhaps the best way to cover them would be not to represent them as heresies, but instead to implement traits to represent the sects, similar to Dharmic religious branches? Supposedly, at the time of the game there were three major Manichaean sects:
* The Mihriyands, who were the largest of the three groups, were centered in Iraq and central Iran, followed an Archegos based in Baghdad, and were very open to outside inflence and freely adopted Muslim names and dress;
* The Miqlasi, who seem to have flourished in Media and Kurdistan, and were strict adherants to Manichaean/Persian ritual and custom;
* And the Denawars, who were centered in the eastern Iranian lands, were responsible for spreading Manichaeanism among the Uyghurs and into China, were the longest-lasting branch of Manichaeanism, and held a middle-of-the-road position between the ultra-orthodox Miqlasi and the Islamising Mihriyands, being strict in their adherence to Manichaean/Persian ritual and custom, but still willing to give concessions to local customs of the converted Uyghurs and Chinese.
I could see the different Manichaean sects being represented via traits akin to the Dharmic religious branches: Mihriyands could have opinion boost with other religions (and possibly the ability to acquire sympathy to a local religion), Denawars could have a bonus to proselytizing, and Miqlasi could have a church opinion/monthly piety bonus.
In addition, it might be a good idea to allow Manicheans (and several other religions) to choose to become vegetarian, granting them "Vegetarian" trait. Considering that vegetarianism is represented in many in-game religions and heresies either as a core tenet (like in Dharmic religions, Mazdaki, Qarmatian and Catharism) or as an idealized lifestyle choice (like Judaism, Taoism and Zoroastrianism), implementing vegetarian trait and vegetarian flavour events would enable those features to be utilized in several religions which practiced it.
And finally, while some ideas for how to represent the division between the Hearers/lay followers and the Elect/monks and nuns, an alternative way to represent the division of the Manichaean faithful would be to represent the Hearers and the Elect via a "caste" system akin to The Winter King mod. Characters with the "Elect" trait would get piety and learning bonuses with a malus to income and fertility, while characters with the "Hearer" trait would get a bonus to taxation and prestige. The traits would be partially hereditary; children of Elect would get the option to join the Elect upon childhood, but not firmly; pious and virtuous Hearers could become Elect, while Elect that fall to material temptations may be demoted to the ranks of the Hearers.